Full wwpdb X-ray Structure Validation Report i
|
|
- Lorin Barnett
- 5 years ago
- Views:
Transcription
1 Full wwpdb X-ray Structure Validation Report i Mar 10, :51 am GMT PDB ID : 1G59 Title : GLUTAMYL-TRNA SYNTHETASE COMPLEXED WITH TRNA(GLU). Authors : Sekine, S.; Nureki, O.; Shimada, A.; Vassylyev, D.G.; Yokoyama, S.; RIKEN Structural Genomics/Proteomics Initiative (RSGI) Deposited on : Resolution : 2.40 Å(reported) This is a Full wwpdb X-ray Structure Validation Report for a publicly released PDB entry. We welcome your comments at validation@mail.wwpdb.org A user guide is available at with specific help available everywhere you see the i symbol. The following versions of software and data (see references i ) were used in the production of this report: MolProbity : 4.02b-467 Xtriage (Phenix) : 1.13 EDS : trunk30967 Percentile statistics : v01 (using entries in the PDB archive December 27th 2017) Refmac : CCP4 : 7.0 (Gargrove) Ideal geometry (proteins) : Engh & Huber (2001) Ideal geometry (DNA, RNA) : Parkinson et al. (1996) Validation Pipeline (wwpdb-vp) : trunk30967
2 Page 2 Full wwpdb X-ray Structure Validation Report 1G59 1 Overall quality at a glance i The following experimental techniques were used to determine the structure: X-RAY DIFFRACTION The reported resolution of this entry is 2.40 Å. Percentile scores (ranging between 0-100) for global validation metrics of the entry are shown in the following graphic. The table shows the number of entries on which the scores are based. Metric Whole archive Similar resolution (#Entries) (#Entries, resolution range(å)) R free ( ) Clashscore ( ) Ramachandran outliers ( ) Sidechain outliers ( ) RSRZ outliers ( ) RNA backbone ( ) The table below summarises the geometric issues observed across the polymeric chains and their fit to the electron density. The red, orange, yellow and green segments on the lower bar indicate the fraction of residues that contain outliers for >=3, 2, 1 and 0 types of geometric quality criteria. A grey segment represents the fraction of residues that are not modelled. The numeric value for each fraction is indicated below the corresponding segment, with a dot representing fractions <=5% The upper red bar (where present) indicates the fraction of residues that have poor fit to the electron density. The numeric value is given above the bar. Mol Chain Length Quality of chain 1 B 75 1 D 75 2 A C 468
3 Page 3 Full wwpdb X-ray Structure Validation Report 1G59 2 Entry composition i There are 3 unique types of molecules in this entry. The entry contains atoms, of which 0 are hydrogens and 0 are deuteriums. In the tables below, the ZeroOcc column contains the number of atoms modelled with zero occupancy, the AltConf column contains the number of residues with at least one atom in alternate conformation and the Trace column contains the number of residues modelled with at most 2 atoms. Molecule 1 is a RNA chain called TRNA(GLU). Mol Chain Residues Atoms ZeroOcc AltConf Trace 1 B 75 Total C N O P D 75 Total C N O P Molecule 2 is a protein called GLUTAMYL-TRNA SYNTHETASE. Mol Chain Residues Atoms ZeroOcc AltConf Trace 2 A 468 Total C N O S C 468 Total C N O S Molecule 3 is water. Mol Chain Residues Atoms ZeroOcc AltConf 3 B 34 Total O D 39 Total O A 107 Total O C 92 Total O
4 Page 4 Full wwpdb X-ray Structure Validation Report 1G59 3 Residue-property plots i These plots are drawn for all protein, RNA and DNA chains in the entry. The first graphic for a chain summarises the proportions of the various outlier classes displayed in the second graphic. The second graphic shows the sequence view annotated by issues in geometryand electron density. Residues are color-coded according to the number of geometric quality criteria for which they contain at least one outlier: green = 0, yellow = 1, orange = 2 and red = 3 or more. A red dot above a residue indicates a poor fit to the electron density (RSRZ > 2). Stretches of 2 or more consecutive residues without any outlier are shown as a green connector. Residues present in the sample, but not in the model, are shown in grey. Molecule 1: TRNA(GLU) Chain B: C563 C564 C565 U566 G567 G568 G569 G570 U571 C572 A573 C574 C575 A576 G501 G502 C503 C504 C505 C506 A507 U508 C509 G510 U511 C512 U513 A514 G515 C516 G517 G518 U519 U520 A521 G522 G523 A524 C525 G526 C527 G528 G529 C530 C531 C532 U533 C534 U535 C536 G539 G540 C541 C542 G543 A544 A545 A546 C548 G549 G550 G551 G552 G553 U554 U555 C556 G557 A558 U559 U560 C561 C562 Molecule 1: TRNA(GLU) Chain D: C563 C564 C565 U566 G567 G568 G569 G570 U571 C572 A573 C574 C575 A576 G501 G502 C503 C504 C505 C506 A507 U508 C509 G510 U511 C512 U513 A514 G515 C516 G517 G518 U519 U520 A521 G522 G523 A524 C525 G526 C527 G528 G529 C530 C531 C532 U533 C534 U535 C536 G539 G540 C541 C542 G543 A544 A545 A546 C548 G549 G550 G551 G552 G553 U554 U555 C556 G557 A558 U559 U560 C561 C562 Molecule 2: GLUTAMYL-TRNA SYNTHETASE Chain A: G280 R281 E282 I283 F284 T285 L286 E287 E288 F289 I290 F293 T294 W295 E296 R297 V298 S299 G302 P303 V304 L307 L310 R311 W312 M313 N314 G315 K316 Y317 I318 R319 E320 V321 L322 E325 E326 V327 R330 V331 K332 P333 F334 L335 R336 L340 S341 W342 E343 S344 E345 L348 V211 S212 T213 P214 I215 H216 V217 L218 L219 Y220 R221 W225 E226 A227 P228 R229 F230 Y231 H232 M233 P234 L235 L236 R237 N238 P239 D240 K241 T242 K243 I244 S245 K246 R247 H250 T251 W255 Y256 K257 A258 E259 G260 F261 L262 A265 L266 R267 N268 Y269 L270 C271 L272 F275 D279 I146 R147 V150 P151 R152 P153 E157 V158 K159 D160 R163 G164 V165 V166 V167 Y168 D169 N170 Q171 E172 I173 P174 D175 V176 V177 L178 L179 K180 S181 Y184 P185 T186 Y187 H188 L189 A190 N191 V192 V193 D194 D195 H196 L197 M198 G199 V200 T201 D202 V203 I204 R205 A206 E207 E208 W209 L210 P79 Y80 R81 Q82 S83 E84 R85 L86 P87 L88 Y89 Q90 K91 Y92 E95 L96 L97 K98 R99 G100 W101 A105 F106 E107 E110 E111 L112 E113 Q114 I115 R116 K117 E118 K119 G120 G121 Y122 D123 G124 R127 P131 E132 E133 A134 E135 E136 R137 A138 R139 R140 G141 E142 P143 H144 V145 M1 V2 V3 T4 R5 I6 A7 P8 S9 P10 T11 G12 D13 P14 H15 Y20 F24 N25 R30 R31 G34 R35 F36 I37 V38 R39 I40 T43 D44 R45 A46 R47 Y48 V49 P50 G51 A52 E53 E54 R55 I56 L60 S66 E69 D72 V73 A74 A75 P76 T77 G78
5 Page 5 Full wwpdb X-ray Structure Validation Report 1G59 R349 R350 A351 V352 E353 L354 M355 R356 P357 R358 F359 D360 T361 E364 F365 P366 E367 K368 A369 R370 Y371 L372 E375 D376 K382 A383 Q384 R385 K386 L387 E388 L391 P392 L393 L394 K395 E396 L397 Y398 P399 R400 L401 R402 A403 Q404 E405 E406 W407 L412 E413 A414 L415 L416 R417 E422 K423 G424 V425 K426 L427 G428 Q429 V430 A431 Q432 P433 L434 R435 A436 A437 L438 S441 L442 E443 T444 P445 G446 L447 F448 E449 I450 L451 L454 G455 K456 E457 R458 A459 L460 R461 R462 L463 E464 R465 A466 L467 A468 Molecule 2: GLUTAMYL-TRNA SYNTHETASE Chain C: M1 V2 V3 T4 R5 I6 A7 P8 S9 P10 D13 G17 Y20 I21 A22 N25 R31 N32 R35 F36 I37 V38 R39 I40 E41 D42 T43 D44 R45 A46 R47 Y48 G51 A52 E53 E54 R55 I56 L57 L60 K61 S66 E69 G70 P71 D72 V73 A74 A75 P76 T77 G78 P79 Y80 R81 Q82 S83 E84 R85 L86 P87 L88 Y89 Q90 K91 Y92 E95 L96 L97 K98 R99 G100 W101 A102 A105 F106 E107 T108 P109 E110 E111 L112 E113 Q114 I115 R116 K117 E118 K119 G120 G121 Y122 D123 G124 R125 A126 R127 N128 I129 P130 P131 E132 E133 A134 E135 E136 R137 A138 R139 R140 G141 E142 P143 H144 R147 L148 K149 R152 P153 G154 T155 T156 E157 V158 K159 D160 E161 L162 R163 G164 V165 V166 V167 Y168 D169 N170 Q171 E172 D175 V176 V177 L178 L179 K180 S181 Y184 P185 H188 L189 A190 N191 V192 V193 D194 D195 H196 L197 V200 V203 I204 R205 A206 E207 E208 W209 L210 V211 S212 T213 P214 I215 H216 V217 L218 L219 Y220 R221 W225 P228 R229 F230 Y231 H232 L235 L236 R237 N238 P239 D240 K241 T242 K243 I244 S245 K246 R247 K248 E259 G260 F261 L262 A265 L266 R267 N268 Y269 L270 C271 L272 M273 S276 M277 R281 F284 T285 L286 E287 E288 F289 I290 Q291 T294 W295 E296 R297 G302 P303 V304 L307 E308 K309 L310 R311 W312 M313 N314 G315 K316 Y317 I318 R319 E320 S323 L324 E325 E326 V327 R330 V331 K332 P333 F334 L335 R336 E337 L340 S341 L348 R349 R350 A351 V352 E353 L354 M355 R356 P357 R358 F359 D360 T361 L362 K363 E364 F365 P366 E367 K368 A369 R370 Y371 L372 E375 P378 K382 A383 Q384 R385 K386 L387 E388 E389 G390 L391 P392 L393 L394 K395 E396 L397 Y398 P399 R400 L401 R402 A403 Q404 E405 E406 W407 T408 A411 L412 E413 A414 L415 L416 F419 E422 K423 G424 V425 K426 L427 G428 Q429 Q432 P433 L434 R435 A436 A437 L438 S441 L442 E443 T444 P445 G446 L447 F448 E449 I450 L451 L454 G455 K456 E457 R458 A459 L460 R461 R462 L463 E464 R465 A468
6 Page 6 Full wwpdb X-ray Structure Validation Report 1G59 4 Data and refinement statistics i Property Value Source Space group C Depositor Cell constants Å Å Å a, b, c, α, β, γ Depositor Resolution (Å) Depositor EDS % Data completeness (in resolution range) 88.4 ( ) 88.4 ( ) Depositor EDS R merge 0.11 Depositor R sym 0.11 Depositor < I/σ(I) > (at 2.39Å) Xtriage Refinement program X-PLOR 3.1 Depositor 0.218, Depositor R, R free 0.219, DCC R free test set 2847 reflections (5.06%) wwpdb-vp Wilson B-factor (Å 2 ) 29.2 Xtriage Anisotropy Xtriage Bulk solvent k sol (e/å 3 ), B sol (Å 2 ) 0.32, 71.2 EDS L-test for twinning 2 < L > = 0.43, < L 2 > = 0.26 Xtriage Estimated twinning fraction No twinning to report. Xtriage F o,f c correlation 0.92 EDS Total number of atoms wwpdb-vp Average B, all atoms (Å 2 ) 36.0 wwpdb-vp Xtriage s analysis on translational NCS is as follows: The largest off-origin peak in the Patterson function is 15.32% of the height of the origin peak. No significant pseudotranslation is detected. 1 Intensities estimated from amplitudes. 2 Theoretical values of < L >, < L 2 > for acentric reflections are 0.5, respectively for untwinned datasets, and 0.375, 0.2 for perfectly twinned datasets.
7 Page 7 Full wwpdb X-ray Structure Validation Report 1G59 5 Model quality i 5.1 Standard geometry i The Z score for a bond length (or angle) is the number of standard deviations the observed value is removed from the expected value. A bond length (or angle) with Z > 5 is considered an outlier worth inspection. RMSZ is the root-mean-square of all Z scores of the bond lengths (or angles). Mol Chain Bond lengths Bond angles RMSZ # Z >5 RMSZ # Z >5 1 B /1782 (1.0%) /2774 (1.9%) 1 D /1782 (1.4%) /2774 (1.9%) 2 A / /5292 (0.0%) 2 C / /5292 All All /11380 (0.4%) /16132 (0.7%) Chiral center outliers are detected by calculating the chiral volume of a chiral center and verifying if the center is modelled as a planar moiety or with the opposite hand.a planarity outlier is detected by checking planarity of atoms in a peptide group, atoms in a mainchain group or atoms of a sidechain that are expected to be planar. Mol Chain #Chirality outliers #Planarity outliers 1 D C 0 1 All All 0 2 All (43) bond length outliers are listed below: Mol Chain Res Type Atoms Z Observed(Å) Ideal(Å) 1 D 557 G P-O B 557 G P-O B 526 G C3 -C D 549 G C3 -C B 555 U C3 -C B 536 C C3 -C B 549 G C3 -C D 535 U C3 -C D 514 A C3 -C B 522 G C3 -C B 517 G O3 -P D 518 G C5 -C D 522 G C3 -C D 512 C C3 -C
8 Page 8 Full wwpdb X-ray Structure Validation Report 1G59 Mol Chain Res Type Atoms Z Observed(Å) Ideal(Å) 1 B 505 C P-O B 511 U C3 -C B 523 G C3 -C B 518 G P-O D 555 U C3 -C D 504 C C3 -C B 504 C C3 -C B 540 G C3 -C B 556 C C4 -C B 524 A C3 -C D 557 G O3 -P D 558 A O3 -P B 535 U C3 -C D 541 C C3 -C D 568 G C3 -C D 554 U C3 -C D 536 C C3 -C D 508 U C3 -C D 555 U P-O D 556 C C4-C D 526 G C3 -C D 506 C C3 -C D 545 A C3 -C D 510 G C3 -C B 535 U C4 -C B 569 G C3 -C D 527 C C3 -C D 558 A C3 -O D 528 G C4 -C All (108) bond angle outliers are listed below: Mol Chain Res Type Atoms Z Observed( o ) Ideal( o ) 1 D 556 C C3 -C2 -C D 576 A C3 -C2 -C D 557 G C3 -C2 -C D 558 A C3 -C2 -C B 576 A C3 -C2 -C D 575 C C3 -C2 -C D 572 C C3 -C2 -C B 515 G C3 -C2 -C D 515 G C3 -C2 -C
9 Page 9 Full wwpdb X-ray Structure Validation Report 1G59 Mol Chain Res Type Atoms Z Observed( o ) Ideal( o ) 1 B 556 C C3 -C2 -C D 560 U C3 -C2 -C B 517 G C3 -C2 -C B 518 G C3 -C2 -C D 518 G C3 -C2 -C D 557 G N9-C1 -C B 575 C C3 -C2 -C B 573 A C3 -C2 -C B 558 A C3 -C2 -C D 520 U C3 -C2 -C D 517 G C3 -C2 -C D 559 U C3 -C2 -C D 569 G C3 -C2 -C B 563 C C3 -C2 -C D 563 C C3 -C2 -C D 532 C C3 -C2 -C D 574 C C3 -C2 -C B 520 U C3 -C2 -C D 571 U C3 -C2 -C D 570 G C3 -C2 -C D 506 C C3 -C2 -C D 541 C O4 -C1 -N B 533 U C3 -C2 -C B 529 G O4 -C1 -N D 567 G C3 -C2 -C B 507 A C3 -C2 -C D 552 G C3 -C2 -C D 573 A C3 -C2 -C D 571 U O4 -C1 -N D 529 G O4 -C1 -N D 519 U C3 -C2 -C D 514 A C3 -C2 -C B 519 U C3 -C2 -C D 564 C C3 -C2 -C B 506 C C3 -C2 -C B 532 C C3 -C2 -C B 560 U O4 -C1 -N D 561 C C3 -C2 -C D 545 A O4 -C1 -N B 559 U C3 -C2 -C B 566 U C3 -C2 -C B 540 G C3 -C2 -C
10 Page 10 Full wwpdb X-ray Structure Validation Report 1G59 Mol Chain Res Type Atoms Z Observed( o ) Ideal( o ) 1 D 550 G C3 -C2 -C B 539 G C3 -C2 -C B 545 A N9-C1 -C D 553 G C3 -C2 -C D 558 A P-O3 -C B 560 U C3 -C2 -C D 568 G C3 -C2 -C D 507 A C3 -C2 -C B 568 G C3 -C2 -C B 551 G C3 -C2 -C B 513 U O4 -C1 -N B 552 G C3 -C2 -C D 562 C C3 -C2 -C D 504 C O4 -C1 -N B 562 C C3 -C2 -C D 504 C C3 -C2 -C D 533 U C3 -C2 -C B 567 G C3 -C2 -C D 509 C C3 -C2 -C B 570 G C3 -C2 -C D 550 G O4 -C1 -N B 508 U C3 -C2 -C B 516 C P-O3 -C B 571 U C3 -C2 -C D 526 G O4 -C1 -N B 528 G O4 -C1 -N D 551 G C3 -C2 -C B 504 C C3 -C2 -C B 555 U O4 -C1 -N B 514 A C3 -C2 -C D 560 U O4 -C1 -N B 553 G C3 -C2 -C B 545 A O4 -C1 -N B 564 C C3 -C2 -C B 546 A C3 -C2 -C D 539 G C3 -C2 -C D 523 G C3 -C2 -C B 550 G C3 -C2 -C D 565 C C3 -C2 -C B 501 G C3 -C2 -C B 524 A O4 -C1 -N D 519 U O4 -C1 -N
11 Page 11 Full wwpdb X-ray Structure Validation Report 1G59 Mol Chain Res Type Atoms Z Observed( o ) Ideal( o ) 2 A 322 LEU CA-CB-CG D 566 U C3 -C2 -C D 545 A N9-C1 -C D 508 U C3 -C2 -C D 540 G C3 -C2 -C B 561 C C3 -C2 -C B 523 G C3 -C2 -C B 504 C O4 -C1 -N B 572 C C3 -C2 -C D 516 C C3 -C2 -C B 542 C O4 -C1 -N B 509 C C3 -C2 -C B 513 U C3 -C2 -C B 565 C C3 -C2 -C B 523 G O4 -C1 -N There are no chirality outliers. All (2) planarity outliers are listed below: Mol Chain Res Type Group 2 C 269 TYR Sidechain 1 D 557 G Sidechain 5.2 Too-close contacts i In the following table, the Non-H and H(model) columns list the number of non-hydrogen atoms and hydrogen atoms in the chain respectively. The H(added) column lists the number of hydrogen atoms added and optimized by MolProbity. The Clashes column lists the number of clashes within the asymmetric unit, whereas Symm-Clashes lists symmetry related clashes. Mol Chain Non-H H(model) H(added) Clashes Symm-Clashes 1 B D A C A B C D All All
12 Page 12 Full wwpdb X-ray Structure Validation Report 1G59 The all-atom clashscore is defined as the number of clashes found per 1000 atoms (including hydrogen atoms). The all-atom clashscore for this structure is 46. All (929) close contacts within the same asymmetric unit are listed below, sorted by their clash magnitude. Atom-1 Atom-2 Interatomic Clash distance (Å) overlap (Å) 1:D:517:G:N2 1:D:557:G:H :B:575:C:H5 2:A:47:ARG:HH :C:37:ILE:HG23 2:C:69:GLU:HB :A:445:PRO:HG2 2:A:450:ILE:HD :A:4:THR:HB 2:A:25:ASN:HD :C:4:THR:HB 2:C:25:ASN:HD :C:240:ASP:OD1 2:C:242:THR:HG :C:262:LEU:H 2:C:314:ASN:HD :C:267:ARG:HD2 2:C:286:LEU:HG :A:262:LEU:H 2:A:314:ASN:HD :D:563:C:H2 1:D:564:C:C :A:112:LEU:HD23 2:A:115:ILE:HD :D:574:C:H4 1:D:575:C:OP :B:550:G:O2 1:B:551:G:H :A:460:LEU:O 2:A:464:GLU:HG :A:77:THR:HG21 2:A:198:MET:HA :C:130:PRO:HG2 2:C:133:GLU:HB :A:1:MET:HE3 2:A:35:ARG:HD :D:535:U:H4 2:C:432:GLN:HE :B:556:C:C2 1:B:557:G:H :D:550:G:O2 1:D:551:G:H :A:445:PRO:HG2 2:A:450:ILE:CD :C:238:ASN:HD22 2:C:242:THR:HG :A:375:GLU:HG3 2:A:465:ARG:NH :B:557:G:H5 1:B:557:G:H :A:205:ARG:HD3 2:A:232:HIS:CE :D:556:C:O2 1:D:556:C:H :A:205:ARG:HD3 2:A:232:HIS:HE :A:294:THR:HG22 2:A:296:GLU:H :A:111:GLU:O 2:A:115:ILE:HG :C:137:ARG:O 2:C:142:GLU:HB :C:75:ALA:HB3 2:C:80:TYR:CZ :A:404:GLN:HG3 2:A:415:LEU:HD :A:153:PRO:HD2 3:A:506:HOH:O :A:205:ARG:HG3 2:A:209:TRP:HD :B:563:C:H2 1:B:564:C:C :C:307:LEU:O 2:C:311:ARG:HG
13 Page 13 Full wwpdb X-ray Structure Validation Report 1G59 Atom-1 Atom-2 Interatomic Clash distance (Å) overlap (Å) 2:C:369:ALA:HB1 2:C:372:LEU:HD :A:398:TYR:HD1 2:A:463:LEU:HD :B:517:G:N2 1:B:557:G:H :A:349:ARG:HG2 2:A:349:ARG:HH :A:444:THR:HG23 2:A:445:PRO:HD :A:384:GLN:HE21 2:A:388:GLU:HG :D:564:C:H2 1:D:565:C:H :C:3:VAL:CG1 2:C:37:ILE:HD :C:463:LEU:C 2:C:463:LEU:HD :A:404:GLN:CG 2:A:415:LEU:HD :B:556:C:H2 1:B:557:G:H :A:407:TRP:CE2 2:A:456:LYS:HA :A:152:ARG:HA 2:A:152:ARG:HH :D:563:C:H2 1:D:564:C:H :A:73:VAL:HG12 2:A:73:VAL:O :C:237:ARG:NH1 2:C:302:GLY:HA :D:564:C:H2 1:D:565:C:C :D:565:C:H2 1:D:566:U:C :A:333:PRO:HD3 3:A:493:HOH:O :C:205:ARG:HG3 2:C:209:TRP:HD :C:137:ARG:HH11 2:C:137:ARG:HB :C:325:GLU:HG3 2:C:349:ARG:HE :D:535:U:C4 2:C:432:GLN:HE :D:555:U:H5 3:D:247:HOH:O :D:517:G:H21 1:D:557:G:H :C:95:GLU:O 2:C:99:ARG:HB :A:391:LEU:HD23 2:A:395:LYS:HE :C:157:GLU:HG2 2:C:167:VAL:HG :A:267:ARG:HD3 3:A:529:HOH:O :A:205:ARG:HG3 2:A:209:TRP:CD :B:570:G:H2 1:B:571:U:C :A:30:ARG:HB3 2:A:290:ILE:HD :C:262:LEU:N 2:C:314:ASN:HD :D:553:G:C2 1:D:554:U:H :A:397:LEU:HG 2:A:401:LEU:HD :B:566:U:O2 1:B:567:G:H :A:226:GLU:HA 3:A:547:HOH:O :D:517:G:N2 1:D:557:G:C :C:205:ARG:HD3 2:C:232:HIS:CE :A:445:PRO:CG 2:A:450:ILE:HD :C:2:VAL:HG21 2:C:32:ASN:HD
14 Page 14 Full wwpdb X-ray Structure Validation Report 1G59 Atom-1 Atom-2 Interatomic Clash distance (Å) overlap (Å) 2:A:262:LEU:H 2:A:314:ASN:ND :B:562:C:O2 1:B:563:C:H :D:519:U:H2 1:D:521:A:OP :A:236:LEU:O 2:A:244:ILE:HG :D:512:C:OP1 2:C:304:VAL:HG :D:556:C:H5 3:D:255:HOH:O :C:385:ARG:O 2:C:389:GLU:HB :C:454:LEU:O 2:C:458:ARG:HD :B:575:C:H5 2:A:47:ARG:NH :A:261:PHE:CE2 2:A:310:LEU:HD :C:169:ASP:O 2:C:172:GLU:HG :B:565:C:O2 1:B:566:U:H :C:137:ARG:HH11 2:C:137:ARG:CB :A:454:LEU:HD23 2:A:458:ARG:HE :A:95:GLU:O 2:A:99:ARG:HB :B:564:C:H2 1:B:565:C:C :B:558:A:H4 1:B:559:U:OP :B:564:C:H2 1:B:565:C:H :D:567:G:O2 1:D:568:G:H :B:563:C:H2 1:B:564:C:H :C:236:LEU:HB2 2:C:244:ILE:HD :C:262:LEU:HD22 2:C:330:ARG:HH :A:163:ARG:NH2 2:A:232:HIS:O :C:393:LEU:HD22 2:C:419:PHE:CE :A:262:LEU:N 2:A:314:ASN:HD :A:383:ALA:HA 2:A:442:LEU:HD :B:517:G:O2 1:B:557:G:N :B:569:G:O2 1:B:570:G:H :C:163:ARG:NH2 2:C:232:HIS:O :C:391:LEU:N 2:C:392:PRO:HD :D:565:C:H2 1:D:566:U:H :C:75:ALA:HB3 2:C:80:TYR:OH :A:39:ARG:NH2 2:A:195:ASP:OD :B:566:U:H2 1:B:567:G:H :C:426:LYS:HB2 2:C:429:GLN:NE :C:444:THR:HG23 2:C:445:PRO:HD :C:8:PRO:HD2 2:C:39:ARG:O :C:235:LEU:O 2:C:237:ARG:HD :C:393:LEU:HD22 2:C:419:PHE:HE :B:576:A:O2 2:A:181:SER:HB :C:106:PHE:CD2 2:C:144:HIS:HB
15 Page 15 Full wwpdb X-ray Structure Validation Report 1G59 Atom-1 Atom-2 Interatomic Clash distance (Å) overlap (Å) 2:A:349:ARG:NH2 2:A:349:ARG:HG :A:375:GLU:HG3 2:A:465:ARG:HH :B:512:C:OP1 2:A:304:VAL:HG :D:562:C:O2 1:D:563:C:H :B:544:A:O2 1:B:545:A:H :A:262:LEU:HD13 2:A:330:ARG:NH :B:557:G:C8 1:B:557:G:H :C:157:GLU:CG 2:C:167:VAL:HG :C:391:LEU:O 2:C:395:LYS:HG :B:553:G:C2 1:B:554:U:H :C:110:GLU:O 2:C:114:GLN:HG :C:158:VAL:HG22 2:C:217:VAL:HG :C:445:PRO:HG2 2:C:450:ILE:HD :A:348:LEU:O 2:A:352:VAL:HG :C:267:ARG:HD3 3:C:484:HOH:O :C:355:MET:HE1 2:C:445:PRO:HD :D:557:G:H8 1:D:557:G:H :A:349:ARG:CG 2:A:349:ARG:HH :C:4:THR:HB 2:C:25:ASN:ND :D:565:C:O2 1:D:566:U:H :D:561:C:H2 1:D:562:C:C :A:132:GLU:HA 2:A:132:GLU:OE :C:285:THR:OG1 2:C:288:GLU:HG :D:556:C:O2 1:D:557:G:H :D:566:U:H2 1:D:567:G:H :D:569:G:O2 1:D:570:G:H :C:205:ARG:HG3 2:C:209:TRP:CD :A:340:LEU:HD21 2:A:370:ARG:NH :C:107:GLU:N 2:C:107:GLU:OE :D:544:A:O2 1:D:545:A:H :C:458:ARG:HH11 2:C:458:ARG:CG :A:370:ARG:HG3 2:A:370:ARG:HH :B:570:G:H2 1:B:571:U:H :C:262:LEU:H 2:C:314:ASN:ND :A:444:THR:HG23 2:A:445:PRO:CD :A:81:ARG:HB3 2:A:84:GLU:HG :C:131:PRO:O 2:C:135:GLU:HG :D:566:U:O2 1:D:567:G:H :A:75:ALA:HB1 2:A:76:PRO:HD :A:365:PHE:HB3 2:A:366:PRO:HD :A:116:ARG:HG3 2:A:121:GLY:HA
16 Page 16 Full wwpdb X-ray Structure Validation Report 1G59 Atom-1 Atom-2 Interatomic Clash distance (Å) overlap (Å) 2:A:444:THR:HG22 2:A:445:PRO:O :A:69:GLU:HB3 2:A:75:ALA:CB :A:441:SER:O 2:A:442:LEU:HB :A:7:ALA:HA 2:A:39:ARG:O :A:56:ILE:O 2:A:60:LEU:HG :C:107:GLU:HB2 2:C:112:LEU:HD :A:11:THR:HG22 2:A:47:ARG:O :A:463:LEU:HD22 2:A:463:LEU:O :A:37:ILE:HG23 2:A:69:GLU:HB :B:519:U:H2 1:B:521:A:OP :D:506:C:H2 1:D:507:A:C :C:355:MET:HE2 2:C:355:MET:HA :D:517:G:H4 1:D:518:G:OP :C:140:ARG:HD2 2:C:140:ARG:N :C:111:GLU:O 2:C:115:ILE:HD :C:7:ALA:HA 2:C:39:ARG:O :D:531:C:H2 1:D:532:C:C :A:189:LEU:O 2:A:193:VAL:HG :A:393:LEU:HD23 2:A:394:LEU:N :A:446:GLY:O 2:A:450:ILE:HG :D:562:C:H2 1:D:563:C:C :A:384:GLN:NE2 2:A:388:GLU:HG :C:444:THR:HG22 2:C:445:PRO:O :D:567:G:H2 1:D:568:G:H :C:105:ALA:O 2:C:144:HIS:HB :B:506:C:H2 1:B:507:A:C :B:567:G:O2 1:B:568:G:H :C:355:MET:HE3 2:C:445:PRO:HG :B:565:C:H2 1:B:566:U:C :C:465:ARG:HB3 2:C:465:ARG:HH :D:555:U:C2 1:D:556:C:H :A:69:GLU:HB3 2:A:75:ALA:HB :B:517:G:H21 1:B:557:G:H :A:122:TYR:CE2 2:A:124:GLY:HA :A:139:ARG:C 2:A:141:GLY:H :A:82:GLN:HG3 2:A:89:TYR:OH :B:504:C:H2 1:B:505:C:C :B:550:G:HO2 1:B:551:G:H :A:136:GLU:HG3 2:A:140:ARG:NH :A:213:THR:HA 2:A:216:HIS:HD :C:355:MET:CE 2:C:358:ARG:HD
17 Page 17 Full wwpdb X-ray Structure Validation Report 1G59 Atom-1 Atom-2 Interatomic Clash distance (Å) overlap (Å) 1:D:518:G:H5 1:D:560:U:O :D:569:G:H2 1:D:570:G:H :A:397:LEU:HG 2:A:401:LEU:CD :C:460:LEU:O 2:C:464:GLU:HG :A:401:LEU:HB3 2:A:460:LEU:HD :A:75:ALA:HB3 2:A:80:TYR:CZ :C:51:GLY:O 2:C:54:GLU:HG :C:56:ILE:N 2:C:56:ILE:HD :A:136:GLU:O 2:A:140:ARG:HG :A:240:ASP:OD1 2:A:242:THR:OG :C:148:LEU:HB2 2:C:178:LEU:HD :A:294:THR:HG22 2:A:296:GLU:N :B:562:C:H2 1:B:563:C:C :D:551:G:H2 1:D:552:G:H :C:363:LYS:O 2:C:366:PRO:HD :C:435:ARG:HD2 2:C:442:LEU:HA :D:555:U:H2 1:D:556:C:H :D:566:U:H2 1:D:567:G:C :A:184:TYR:HE1 3:A:487:HOH:O :B:567:G:H2 1:B:568:G:H :C:147:ARG:HG2 2:C:147:ARG:HH :D:543:G:O2 1:D:544:A:H :C:237:ARG:HH11 2:C:302:GLY:HA :C:114:GLN:O 2:C:118:GLU:HG :C:44:ASP:OD2 2:C:47:ARG:HG :A:101:TRP:HH2 3:A:575:HOH:O :A:6:ILE:O 2:A:8:PRO:HD :C:75:ALA:HB1 2:C:76:PRO:HD :D:517:G:O2 1:D:557:G:N :C:162:LEU:HD21 2:C:231:TYR:HD :D:505:C:O2 1:D:506:C:H :B:535:U:C4 2:A:432:GLN:HE :B:543:G:O2 1:B:544:A:H :D:504:C:H2 1:D:505:C:C :C:398:TYR:HB3 2:C:399:PRO:HD :A:391:LEU:CD2 2:A:395:LYS:HE :B:566:U:H2 1:B:567:G:C :B:539:G:O2 1:B:540:G:H :C:109:PRO:HA 2:C:112:LEU:HD :B:552:G:H2 1:B:553:G:O :D:563:C:H2 1:D:564:C:C
18 Page 18 Full wwpdb X-ray Structure Validation Report 1G59 Atom-1 Atom-2 Interatomic Clash distance (Å) overlap (Å) 1:B:568:G:H2 1:B:569:G:H :B:505:C:O2 1:B:506:C:H :A:237:ARG:NH1 2:A:302:GLY:HA :B:561:C:H2 1:B:562:C:C :A:461:ARG:O 2:A:464:GLU:HB :C:229:ARG:HB2 2:C:229:ARG:HH :B:505:C:H2 1:B:506:C:H :B:569:G:H2 1:B:570:G:H :A:398:TYR:CD1 2:A:463:LEU:HD :C:147:ARG:HG2 2:C:147:ARG:NH :C:326:GLU:OE1 2:C:330:ARG:NE :B:576:A:H5 2:A:45:ARG:CZ :A:412:LEU:HG 2:A:451:LEU:HD :A:81:ARG:HB3 2:A:84:GLU:CG :B:517:G:C5 1:B:557:G:C :A:4:THR:HB 2:A:25:ASN:ND :C:236:LEU:HD12 2:C:303:PRO:HG :D:505:C:H2 1:D:506:C:H :A:333:PRO:HG3 2:A:336:ARG:NH :C:115:ILE:O 2:C:119:LYS:HG :C:324:LEU:HD11 2:C:353:GLU:HB :A:202:ASP:OD1 2:A:229:ARG:HD :B:526:G:O2 1:B:527:C:H :C:316:LYS:HE3 2:C:320:GLU:CD :B:502:G:H2 1:B:503:C:C :B:517:G:H4 1:B:518:G:OP :C:398:TYR:CE2 2:C:402:ARG:HG :A:92:TYR:O 2:A:95:GLU:HB :A:124:GLY:O 2:A:127:ARG:HB :C:71:PRO:HB3 2:C:81:ARG:NH :C:87:PRO:O 2:C:90:GLN:HB :D:568:G:H2 1:D:569:G:H :A:370:ARG:HG3 2:A:370:ARG:NH :C:89:TYR:CD2 2:C:185:PRO:HG :D:558:A:H4 1:D:559:U:OP :C:378:PRO:HA 3:C:530:HOH:O :C:458:ARG:NH1 2:C:458:ARG:HG :D:501:G:H2 1:D:502:G:C :C:45:ARG:HG2 2:C:184:TYR:CE :C:75:ALA:HB3 2:C:80:TYR:CE :D:503:C:O2 1:D:504:C:H
19 Page 19 Full wwpdb X-ray Structure Validation Report 1G59 Atom-1 Atom-2 Interatomic Clash distance (Å) overlap (Å) 1:D:556:C:C2 1:D:556:C:O :D:564:C:O2 1:D:565:C:H :D:570:G:H2 1:D:571:U:C :A:423:LYS:HB2 2:A:423:LYS:NZ :C:136:GLU:HA 2:C:139:ARG:HD :C:350:ARG:O 2:C:350:ARG:HD :D:502:G:H2 1:D:503:C:C :A:73:VAL:O 2:A:74:ALA:O :B:530:C:H2 1:B:531:C:H :D:534:C:O2 2:C:435:ARG:NH :B:564:C:O2 1:B:565:C:H :D:541:C:O2 1:D:542:C:H :A:170:ASN:HA 2:A:173:ILE:HD :A:333:PRO:HG3 2:A:336:ARG:HH :B:503:C:O2 1:B:504:C:H :C:426:LYS:HB2 2:C:429:GLN:HE :A:116:ARG:CG 2:A:121:GLY:HA :C:423:LYS:NZ 2:C:423:LYS:HB :D:569:G:H4 2:C:237:ARG:HH :C:238:ASN:O 2:C:304:VAL:HG :D:539:G:H2 1:D:540:G:H :C:135:GLU:O 2:C:139:ARG:HD :C:139:ARG:C 2:C:141:GLY:H :D:506:C:OP1 2:C:163:ARG:HG :D:563:C:C2 1:D:564:C:H :B:523:G:O2 1:B:524:A:H :C:211:VAL:O 2:C:214:PRO:HD :C:266:LEU:HD22 2:C:270:LEU:HD :C:435:ARG:NH1 2:C:444:THR:HG :B:531:C:H2 1:B:532:C:C :B:559:U:O2 1:B:560:U:H :A:85:ARG:NH1 2:A:194:ASP:OD :A:327:VAL:HG12 2:A:352:VAL:HG :C:355:MET:HE2 2:C:358:ARG:HD :C:441:SER:O 2:C:442:LEU:HB :D:530:C:H2 1:D:531:C:H :D:539:G:O2 1:D:540:G:H :C:162:LEU:N 2:C:162:LEU:HD :C:160:ASP:OD2 2:C:232:HIS:HD :C:73:VAL:O 2:C:74:ALA:O :A:178:LEU:HB3 2:A:189:LEU:HG
20 Page 20 Full wwpdb X-ray Structure Validation Report 1G59 Atom-1 Atom-2 Interatomic Clash distance (Å) overlap (Å) 2:C:75:ALA:CB 2:C:80:TYR:OH :D:567:G:O2 1:D:568:G:C :C:135:GLU:O 2:C:139:ARG:NH :D:529:G:H2 1:D:530:C:C :D:523:G:H2 1:D:524:A:H :D:531:C:H2 1:D:532:C:H :D:556:C:C2 1:D:557:G:H :D:556:C:C2 1:D:557:G:C :A:407:TRP:CZ2 2:A:456:LYS:HA :A:413:GLU:HG3 2:A:448:PHE:CZ :A:137:ARG:O 2:A:142:GLU:HB :A:139:ARG:HE 2:A:140:ARG:HH :C:220:TYR:CZ 2:C:228:PRO:HD :C:404:GLN:NE2 2:C:415:LEU:HD :D:544:A:C2 1:D:545:A:H :A:75:ALA:HB3 2:A:80:TYR:OH :D:521:A:H61 1:D:546:A:H :A:139:ARG:HB3 2:A:140:ARG:HE :A:75:ALA:HB3 2:A:80:TYR:CE :C:268:ASN:C 2:C:268:ASN:HD :C:276:SER:O 2:C:297:ARG:HD :C:10:PRO:HB3 2:C:53:GLU:HA :C:286:LEU:O 2:C:290:ILE:HG :B:556:C:H2 1:B:556:C:O :C:3:VAL:HG11 2:C:37:ILE:HD :A:52:ALA:O 2:A:56:ILE:HG :B:556:C:H2 1:B:557:G:C :C:205:ARG:O 2:C:232:HIS:HA :A:238:ASN:HB2 2:A:240:ASP:OD :A:450:ILE:HD13 2:A:450:ILE:N :B:530:C:H2 1:B:531:C:C :B:554:U:H2 1:B:555:U:C :C:458:ARG:CB 2:C:458:ARG:HH :D:570:G:H2 1:D:571:U:H :B:525:C:H2 1:B:526:G:C :D:563:C:C2 1:D:564:C:C :C:119:LYS:O 2:C:120:GLY:C :C:116:ARG:HG2 2:C:121:GLY:HA :C:31:ARG:HD2 2:C:31:ARG:O :C:74:ALA:O 2:C:75:ALA:HB :D:552:G:H2 1:D:553:G:O
21 Page 21 Full wwpdb X-ray Structure Validation Report 1G59 Atom-1 Atom-2 Interatomic Clash distance (Å) overlap (Å) 2:A:393:LEU:HA 2:A:396:GLU:HB :D:506:C:H2 1:D:507:A:H :A:330:ARG:O 2:A:333:PRO:HD :B:521:A:H61 1:B:546:A:H :A:114:GLN:O 2:A:118:GLU:HG :C:207:GLU:HA 2:C:232:HIS:HB :D:517:G:C6 1:D:558:A:C :A:152:ARG:NH1 2:A:152:ARG:HA :B:576:A:H5 2:A:45:ARG:NH :C:239:PRO:HA 2:C:304:VAL:CG :A:350:ARG:NH1 2:A:354:LEU:HD :A:398:TYR:N 2:A:399:PRO:HD :A:383:ALA:CA 2:A:442:LEU:HD :D:539:G:H2 1:D:540:G:C :D:571:U:H2 1:D:572:C:C :A:427:LEU:O 2:A:430:VAL:HG :C:260:GLY:HA2 2:C:334:PHE:CZ :C:396:GLU:OE1 2:C:423:LYS:HD :C:458:ARG:HH11 2:C:458:ARG:HB :D:525:C:H2 1:D:526:G:C :D:556:C:H2 1:D:557:G:H :A:350:ARG:O 2:A:350:ARG:HD :A:385:ARG:HH11 2:A:385:ARG:HG :B:551:G:H2 1:B:552:G:H :B:565:C:H2 1:B:566:U:H :C:458:ARG:HH11 2:C:458:ARG:HG :A:206:ALA:HB1 2:A:235:LEU:CD :C:331:VAL:HG21 2:C:365:PHE:CD :A:398:TYR:CE2 2:A:402:ARG:HD :C:446:GLY:O 2:C:450:ILE:HG :A:31:ARG:NH1 2:A:293:PHE:O :C:236:LEU:CB 2:C:244:ILE:HD :C:265:ALA:HB3 2:C:314:ASN:HD :A:105:ALA:HB2 2:A:147:ARG:HD :A:213:THR:N 2:A:214:PRO:HD :A:214:PRO:HA 2:A:217:VAL:HG :B:529:G:H2 1:B:530:C:C :C:236:LEU:HB3 2:C:244:ILE:HG :D:523:G:H2 1:D:524:A:C :D:530:C:O2 1:D:531:C:H :A:170:ASN:N 2:A:170:ASN:HD
22 Page 22 Full wwpdb X-ray Structure Validation Report 1G59 Atom-1 Atom-2 Interatomic Clash distance (Å) overlap (Å) 1:D:559:U:C5 1:D:560:U:C :D:575:C:O4 1:D:575:C:O :B:555:U:H2 1:B:556:C:H :D:526:G:O2 1:D:527:C:H :B:523:G:H2 1:B:524:A:H :B:558:A:O2 1:B:559:U:H :A:152:ARG:NH2 2:A:173:ILE:O :A:74:ALA:O 2:A:75:ALA:HB :B:539:G:H2 1:B:540:G:H :C:111:GLU:O 2:C:114:GLN:HB :C:178:LEU:O 2:C:185:PRO:HA :C:423:LYS:HZ3 2:C:423:LYS:HB :A:267:ARG:CD 3:A:529:HOH:O :B:539:G:H2 1:B:540:G:C :D:553:G:C3 1:D:554:U:H :A:192:VAL:HG13 2:A:220:TYR:CE :A:391:LEU:O 2:A:395:LYS:HG :C:208:GLU:CG 2:C:235:LEU:HD :C:208:GLU:HG3 2:C:235:LEU:HD :A:119:LYS:O 2:A:120:GLY:C :A:131:PRO:O 2:A:135:GLU:HG :C:110:GLU:H 2:C:110:GLU:CD :C:386:LYS:HE2 2:C:432:GLN:HB :B:523:G:H2 1:B:524:A:C :C:463:LEU:O 2:C:463:LEU:HD :D:505:C:H2 1:D:506:C:C :B:502:G:O2 1:B:503:C:H :B:563:C:H2 1:B:564:C:C :C:147:ARG:NH1 2:C:175:ASP:O :C:238:ASN:HB3 2:C:239:PRO:HD :D:553:G:H2 1:D:554:U:H :A:15:HIS:CE1 2:A:251:THR:HB :B:511:U:O2 1:B:512:C:H :B:558:A:H1 1:B:560:U:C :C:412:LEU:O 2:C:416:LEU:HD :C:407:TRP:CE2 2:C:456:LYS:HA :C:57:LEU:O 2:C:61:LYS:HD :D:530:C:H2 1:D:531:C:C :B:568:G:H2 1:B:569:G:C :C:444:THR:HG23 2:C:445:PRO:CD :D:535:U:N3 2:C:444:THR:O
23 Page 23 Full wwpdb X-ray Structure Validation Report 1G59 Atom-1 Atom-2 Interatomic Clash distance (Å) overlap (Å) 2:C:426:LYS:O 2:C:429:GLN:HB :D:516:C:O2 1:D:517:G:P :A:211:VAL:O 2:A:214:PRO:HD :A:285:THR:OG1 2:A:288:GLU:HG :A:152:ARG:HG3 2:A:152:ARG:HH :A:391:LEU:HA 2:A:394:LEU:HD :C:238:ASN:ND2 2:C:248:LYS:HD :A:207:GLU:HA 2:A:232:HIS:HB :A:436:ALA:HB2 2:A:442:LEU:HD :C:270:LEU:O 2:C:273:MET:HB :A:110:GLU:CD 2:A:110:GLU:H :A:407:TRP:NE1 2:A:456:LYS:N :B:517:G:C6 1:B:557:G:C :C:365:PHE:HB3 2:C:366:PRO:HD :C:461:ARG:O 2:C:464:GLU:HB :B:541:C:O2 1:B:542:C:H :A:91:LYS:HG2 2:A:92:TYR:N :B:505:C:H2 1:B:506:C:C :B:544:A:C2 1:B:545:A:H :C:458:ARG:NH1 2:C:458:ARG:CG :A:178:LEU:O 2:A:185:PRO:HA :D:569:G:O2 1:D:570:G:C :D:518:G:C5 1:D:560:U:O :D:551:G:H2 1:D:552:G:C :A:107:GLU:N 2:A:107:GLU:OE :A:188:HIS:HA 2:A:216:HIS:HE :A:238:ASN:O 2:A:304:VAL:HG :D:542:C:O2 1:D:543:G:H :A:147:ARG:HB3 2:A:175:ASP:O :B:556:C:C2 1:B:557:G:C :C:388:GLU:HA 2:C:391:LEU:HD :C:41:GLU:HA 2:C:82:GLN:HG :C:375:GLU:HG3 2:C:465:ARG:HH :A:435:ARG:HD2 2:A:444:THR:HB :A:73:VAL:CG1 2:A:73:VAL:O :A:77:THR:HG22 2:A:77:THR:O :A:92:TYR:CE2 2:A:225:TRP:HH :A:286:LEU:O 2:A:290:ILE:HG :A:307:LEU:O 2:A:311:ARG:HG :B:556:C:C3 1:B:557:G:C :D:561:C:H2 1:D:562:C:C
24 Page 24 Full wwpdb X-ray Structure Validation Report 1G59 Atom-1 Atom-2 Interatomic Clash distance (Å) overlap (Å) 2:A:311:ARG:HH11 2:A:311:ARG:HB :A:3:VAL:HB 2:A:200:VAL:HA :C:122:TYR:CE2 2:C:124:GLY:HA :C:435:ARG:HD3 2:C:444:THR:HB :A:152:ARG:NH1 2:A:152:ARG:HG :A:279:ASP:OD2 2:A:281:ARG:HB :A:316:LYS:HE2 2:A:320:GLU:CD :A:401:LEU:CB 2:A:460:LEU:HD :B:525:C:H2 1:B:526:G:H :B:556:C:C3 1:B:557:G:H :B:518:G:N2 1:B:557:G:H :D:556:C:C2 1:D:557:G:H :A:262:LEU:HB2 2:A:314:ASN:ND :A:86:LEU:HA 2:A:89:TYR:HD :B:506:C:H2 1:B:507:A:H :C:326:GLU:O 2:C:330:ARG:HG :A:262:LEU:HB2 2:A:314:ASN:HD :C:169:ASP:OD2 2:C:171:GLN:HB :C:208:GLU:HG2 2:C:235:LEU:HD :C:229:ARG:CG 2:C:229:ARG:HH :A:112:LEU:HA 2:A:115:ILE:HD :A:44:ASP:O 2:A:46:ALA:N :C:239:PRO:HD3 3:C:478:HOH:O :C:71:PRO:HB3 2:C:81:ARG:HH :A:262:LEU:HD13 2:A:330:ARG:HH :C:330:ARG:HD3 3:C:509:HOH:O :D:517:G:C4 1:D:558:A:C :A:194:ASP:O 2:A:198:MET:HB :C:355:MET:HE1 2:C:358:ARG:HD :A:417:ARG:NH1 2:A:427:LEU:HD :D:517:G:C2 1:D:558:A:C :C:426:LYS:H 2:C:429:GLN:NE :C:261:PHE:CE2 2:C:310:LEU:HD :C:385:ARG:HH11 2:C:385:ARG:CB :B:508:U:C2 1:B:515:G:O :A:423:LYS:HZ3 2:A:423:LYS:HB :B:527:C:H2 1:B:528:G:H :C:135:GLU:HB3 2:C:139:ARG:CZ :C:246:LYS:O 2:C:246:LYS:HE :A:257:LYS:HG2 3:A:507:HOH:O :A:461:ARG:NH2 2:A:462:ARG:HB
25 Page 25 Full wwpdb X-ray Structure Validation Report 1G59 Atom-1 Atom-2 Interatomic Clash distance (Å) overlap (Å) 1:B:518:G:H5 1:B:560:U:O :D:534:C:H5 3:D:70:HOH:O :D:517:G:H22 1:D:557:G:H :B:561:C:H2 1:B:562:C:C :C:422:GLU:HG2 2:C:423:LYS:NZ :C:53:GLU:HG2 2:C:54:GLU:N :A:169:ASP:HB3 2:A:172:GLU:HG :C:195:ASP:HA 2:C:200:VAL:HG :D:517:G:C6 1:D:557:G:C :A:332:LYS:O 2:A:336:ARG:HG :A:404:GLN:HG2 2:A:415:LEU:HD :B:553:G:C3 1:B:554:U:H :C:195:ASP:O 2:C:200:VAL:HG :C:246:LYS:HG3 2:C:247:ARG:N :C:6:ILE:HG13 2:C:6:ILE:O :D:505:C:H4 2:C:163:ARG:HD :A:400:ARG:HH22 2:A:422:GLU:CD :B:504:C:H2 1:B:505:C:H :B:540:G:H2 1:B:541:C:C :C:358:ARG:NH1 2:C:445:PRO:HB :D:508:U:H6 1:D:508:U:O :C:348:LEU:O 2:C:352:VAL:HG :C:79:PRO:HB3 2:C:84:GLU:OE :A:393:LEU:C 2:A:393:LEU:HD :B:542:C:O2 1:B:543:G:H :C:238:ASN:HD22 2:C:242:THR:CG :A:157:GLU:HG3 2:A:167:VAL:HG :C:243:LYS:O 2:C:243:LYS:HG :D:525:C:H2 1:D:526:G:H :D:569:G:H2 1:D:570:G:C :B:562:C:O2 1:B:563:C:C :C:391:LEU:N 2:C:392:PRO:CD :D:525:C:O2 1:D:526:G:H :A:376:ASP:O 2:A:376:ASP:CG :C:116:ARG:HG2 2:C:120:GLY:O :C:5:ARG:HH21 2:C:195:ASP:CG :A:105:ALA:O 2:A:144:HIS:HB :A:157:GLU:HG2 3:A:488:HOH:O :B:508:U:O5 1:B:508:U:H :A:20:TYR:O 2:A:24:PHE:HD :C:406:GLU:HG3 2:C:408:THR:HG
26 Page 26 Full wwpdb X-ray Structure Validation Report 1G59 Atom-1 Atom-2 Interatomic Clash distance (Å) overlap (Å) 1:D:553:G:O2 1:D:554:U:H :A:239:PRO:HA 2:A:304:VAL:HG :C:238:ASN:HD21 2:C:245:SER:N :C:385:ARG:HH11 2:C:385:ARG:HB :C:435:ARG:HH11 2:C:444:THR:CG :A:44:ASP:C 2:A:46:ALA:H :C:265:ALA:CB 2:C:314:ASN:HD :C:267:ARG:NH2 2:C:284:PHE:O :C:465:ARG:O 2:C:468:ALA:HB :C:122:TYR:OH 2:C:125:ARG:HG :C:277:MET:HB2 3:C:549:HOH:O :C:390:GLY:C 2:C:392:PRO:HD :A:386:LYS:HE3 2:A:432:GLN:HG :C:213:THR:O 2:C:217:VAL:HG :A:160:ASP:OD2 2:A:232:HIS:HD :B:556:C:O2 1:B:557:G:H :C:361:THR:O 2:C:364:GLU:HB :D:535:U:H4 2:C:432:GLN:NE :A:314:ASN:HB3 2:A:360:ASP:O :C:196:HIS:HD2 3:C:529:HOH:O :C:236:LEU:O 2:C:244:ILE:HG :C:425:VAL:HG22 2:C:429:GLN:OE :D:511:U:O2 1:D:512:C:H :C:125:ARG:HE 2:C:125:ARG:HB :C:323:SER:OG 2:C:326:GLU:HB :C:3:VAL:HG13 2:C:37:ILE:HD :D:509:C:H4 1:D:510:G:OP :A:396:GLU:OE1 2:A:423:LYS:HE :A:6:ILE:HD11 2:A:38:VAL:HG :B:531:C:H2 1:B:532:C:H :B:530:C:O2 1:B:531:C:H :B:553:G:H2 1:B:554:U:H :B:569:G:H2 1:B:570:G:C :C:463:LEU:CD2 2:C:463:LEU:C :B:573:A:C2 1:B:575:C:N :C:115:ILE:CG2 2:C:122:TYR:HA :C:397:LEU:HG 2:C:401:LEU:HD :D:504:C:H2 1:D:505:C:H :D:517:G:H21 1:D:557:G:C :A:333:PRO:HA 2:A:336:ARG:CZ :B:509:C:H4 1:B:510:G:OP
27 Page 27 Full wwpdb X-ray Structure Validation Report 1G59 Atom-1 Atom-2 Interatomic Clash distance (Å) overlap (Å) 1:B:551:G:H2 1:B:552:G:C :D:561:C:H2 1:D:562:C:H :A:213:THR:HA 2:A:216:HIS:CD :C:17:GLY:O 2:C:20:TYR:HB :D:568:G:H2 1:D:569:G:C :A:463:LEU:HD22 2:A:467:LEU:HG :A:75:ALA:HB1 2:A:76:PRO:CD :C:229:ARG:CB 2:C:229:ARG:HH :C:75:ALA:HB1 2:C:76:PRO:CD :D:555:U:C3 1:D:556:C:H :A:255:TRP:CZ2 2:A:259:GLU:HG :B:562:C:O5 1:B:562:C:H :C:86:LEU:N 2:C:87:PRO:HD :C:96:LEU:HB3 2:C:102:ALA:HB :D:556:C:H2 1:D:557:G:C :A:133:GLU:HG2 2:A:137:ARG:HD :A:176:VAL:HG11 2:A:215:ILE:HD :A:355:MET:HG3 2:A:369:ALA:HB :A:435:ARG:CD 2:A:444:THR:HB :C:281:ARG:HG2 2:C:281:ARG:HH :D:523:G:O2 1:D:524:A:H :A:40:ILE:O 2:A:82:GLN:HB :D:540:G:H2 1:D:541:C:C :D:557:G:C8 1:D:557:G:H :A:69:GLU:CB 2:A:75:ALA:HB :B:552:G:C4 1:B:553:G:C :B:555:U:C2 1:B:556:C:H :C:140:ARG:HD2 2:C:140:ARG:H :C:281:ARG:HG2 2:C:281:ARG:NH :D:556:C:O2 1:D:557:G:C :B:517:G:O6 1:B:555:U:H :C:422:GLU:HG2 2:C:423:LYS:HZ :B:516:C:O2 1:B:517:G:P :D:505:C:O3 2:C:163:ARG:HG :C:238:ASN:HD21 2:C:245:SER:CB :C:401:LEU:CD1 2:C:415:LEU:HD :C:383:ALA:HA 2:C:442:LEU:HD :A:157:GLU:CG 2:A:167:VAL:HG :A:51:GLY:HA2 2:A:54:GLU:OE :B:534:C:H4 2:A:426:LYS:NZ :A:275:PHE:CE2 2:A:297:ARG:HB
28 Page 28 Full wwpdb X-ray Structure Validation Report 1G59 Atom-1 Atom-2 Interatomic Clash distance (Å) overlap (Å) 2:C:441:SER:O 2:C:442:LEU:CB :A:139:ARG:C 2:A:141:GLY:N :A:202:ASP:CG 2:A:229:ARG:HH :B:556:C:O2 1:B:556:C:C :C:110:GLU:N 2:C:110:GLU:OE :A:136:GLU:HA 2:A:140:ARG:NH :A:1:MET:SD 2:A:34:GLY:HA :A:1:MET:CE 2:A:35:ARG:HH :A:438:LEU:O 2:A:462:ARG:HD :C:185:PRO:HB3 2:C:189:LEU:HD :C:323:SER:O 2:C:327:VAL:HG :C:402:ARG:HA 2:C:460:LEU:HD :D:501:G:O5 1:D:501:G:H :A:118:GLU:HG2 2:A:118:GLU:H :A:391:LEU:N 2:A:392:PRO:CD :B:561:C:O2 1:B:562:C:C :D:552:G:C4 1:D:553:G:C :C:355:MET:HA 2:C:358:ARG:HG :C:446:GLY:O 2:C:449:GLU:HG :A:139:ARG:O 2:A:141:GLY:N :A:294:THR:CG2 2:A:296:GLU:HG :C:137:ARG:O 2:C:142:GLU:CB :C:160:ASP:OD1 2:C:162:LEU:HB :C:314:ASN:O 2:C:318:ILE:HG :A:205:ARG:O 2:A:232:HIS:HA :A:250:HIS:HA 3:A:572:HOH:O :A:335:LEU:HD13 2:A:342:TRP:CE :C:107:GLU:HB2 2:C:112:LEU:CD :B:504:C:H3 3:B:82:HOH:O :D:524:A:H2 1:D:525:C:C :A:294:THR:HB 2:A:297:ARG:HG :A:407:TRP:CD1 2:A:456:LYS:N :A:6:ILE:C 2:A:8:PRO:HD :D:556:C:C2 1:D:557:G:C :A:400:ARG:HG2 2:A:400:ARG:H :A:88:LEU:CD1 2:A:92:TYR:HE :B:514:A:C5 1:B:522:G:C :C:178:LEU:HB3 2:C:189:LEU:HG :C:435:ARG:HH11 2:C:444:THR:HG :D:503:C:H2 1:D:504:C:C :D:553:G:H2 1:D:554:U:C
29 Page 29 Full wwpdb X-ray Structure Validation Report 1G59 Atom-1 Atom-2 Interatomic Clash distance (Å) overlap (Å) 2:A:239:PRO:HA 2:A:304:VAL:CG :C:117:LYS:HB2 2:C:117:LYS:NZ :C:147:ARG:CG 2:C:147:ARG:HH :A:203:VAL:HB 2:A:230:PHE:CD :A:358:ARG:CZ 2:A:445:PRO:HA :A:75:ALA:CB 2:A:80:TYR:OH :B:534:C:H6 1:B:534:C:O :D:506:C:P 2:C:163:ARG:HG :D:516:C:O2 1:D:517:G:OP :A:152:ARG:CG 2:A:152:ARG:HH :A:265:ALA:CB 2:A:314:ASN:HD :C:132:GLU:OE1 2:C:136:GLU:HG :C:97:LEU:C 2:C:99:ARG:H :D:520:U:H2 1:D:521:A:H :A:87:PRO:O 2:A:90:GLN:HB :A:88:LEU:HD11 2:A:92:TYR:HE :C:168:TYR:CD2 2:C:214:PRO:HG :C:213:THR:N 2:C:214:PRO:CD :C:382:LYS:HG2 3:C:483:HOH:O :D:520:U:C2 1:D:521:A:H :D:517:G:C2 1:D:558:A:C :D:562:C:H6 1:D:562:C:O :A:86:LEU:N 2:A:87:PRO:CD :C:168:TYR:CE2 2:C:214:PRO:HG :C:203:VAL:HG12 2:C:205:ARG:HD :C:404:GLN:HA 2:C:404:GLN:NE :C:408:THR:OG1 2:C:411:ALA:CB :C:318:ILE:O 2:C:356:ARG:HD :A:354:LEU:HD22 2:A:449:GLU:HG :C:139:ARG:HG3 2:C:139:ARG:NH :C:331:VAL:CG2 2:C:365:PHE:CD :A:202:ASP:OD2 2:A:229:ARG:NH :B:524:A:H2 1:B:525:C:C :C:239:PRO:HA 2:C:304:VAL:HG :D:501:G:H2 1:D:502:G:H :A:13:ASP:N 2:A:13:ASP:OD :A:397:LEU:C 2:A:399:PRO:HD :C:111:GLU:O 2:C:115:ILE:CD :C:426:LYS:HE2 2:C:427:LEU:H :A:139:ARG:HE 2:A:140:ARG:NH :A:89:TYR:CG 2:A:185:PRO:HG
30 Page 30 Full wwpdb X-ray Structure Validation Report 1G59 Atom-1 Atom-2 Interatomic Clash distance (Å) overlap (Å) 2:A:311:ARG:NH1 2:A:311:ARG:HB :B:567:G:O2 1:B:568:G:C :A:206:ALA:HB1 2:A:235:LEU:HD :A:444:THR:CG2 2:A:445:PRO:N :B:501:G:H2 1:B:502:G:C :C:316:LYS:HE3 2:C:320:GLU:OE :D:556:C:C3 1:D:557:G:H :B:509:C:H5 1:B:523:G:O :C:179:LEU:HD23 2:C:179:LEU:HA :D:517:G:C2 1:D:557:G:H :A:107:GLU:HG2 2:A:115:ILE:HD :A:275:PHE:HE2 2:A:297:ARG:HB :A:261:PHE:HZ 2:A:311:ARG:HG :B:569:G:O2 1:B:570:G:C :D:562:C:O2 1:D:563:C:C :A:142:GLU:HG3 2:A:143:PRO:HD :A:246:LYS:HA 2:A:251:THR:HG :A:372:LEU:HD23 2:A:372:LEU:HA :D:502:G:O2 1:D:503:C:H :D:509:C:H5 1:D:523:G:O :A:434:LEU:HD12 2:A:434:LEU:O :A:89:TYR:CD2 2:A:185:PRO:HG :A:202:ASP:CG 2:A:229:ARG:NH :A:30:ARG:CB 2:A:290:ILE:HD :C:262:LEU:HD11 2:C:318:ILE:HG :B:558:A:H2 1:B:560:U:OP :B:563:C:C2 1:B:564:C:H :C:69:GLU:HB3 2:C:75:ALA:HB :D:556:C:C3 1:D:557:G:C :A:75:ALA:N 3:A:566:HOH:O :C:324:LEU:HD23 2:C:324:LEU:O :C:332:LYS:HB2 2:C:333:PRO:CD :D:517:G:C5 1:D:557:G:C :D:508:U:O2 1:D:546:A:H :B:550:G:O2 1:B:551:G:C :C:132:GLU:OE2 2:C:132:GLU:HA :C:310:LEU:O 2:C:313:MET:HB :D:567:G:H2 1:D:568:G:C :B:573:A:H2 1:B:575:C:N :C:124:GLY:O 2:C:127:ARG:HB :C:51:GLY:O 2:C:53:GLU:N
Full wwpdb X-ray Structure Validation Report i
Full wwpdb X-ray Structure Validation Report i Mar 8, 2018 06:13 pm GMT PDB ID : 5G5C Title : Structure of the Pyrococcus furiosus Esterase Pf2001 with space group C2221 Authors : Varejao, N.; Reverter,
More informationFull wwpdb X-ray Structure Validation Report i
Full wwpdb X-ray Structure Validation Report i Mar 13, 2018 04:03 pm GMT PDB ID : 5NMJ Title : Chicken GRIFIN (crystallisation ph: 6.5) Authors : Ruiz, F.M.; Romero, A. Deposited on : 2017-04-06 Resolution
More informationFull wwpdb X-ray Structure Validation Report i
Full wwpdb X-ray Structure Validation Report i Jan 17, 2019 09:42 AM EST PDB ID : 6D3Z Title : Protease SFTI complex Authors : Law, R.H.P.; Wu, G. Deposited on : 2018-04-17 Resolution : 2.00 Å(reported)
More informationFull wwpdb X-ray Structure Validation Report i
Full wwpdb X-ray Structure Validation Report i Jan 28, 2019 11:10 AM EST PDB ID : 6A5H Title : The structure of [4+2] and [6+4] cyclase in the biosynthetic pathway of unidentified natural product Authors
More informationFull wwpdb X-ray Structure Validation Report i
Full wwpdb X-ray Structure Validation Report i Mar 8, 2018 10:24 pm GMT PDB ID : 1A30 Title : HIV-1 PROTEASE COMPLEXED WITH A TRIPEPTIDE INHIBITOR Authors : Louis, J.M.; Dyda, F.; Nashed, N.T.; Kimmel,
More informationFull wwpdb X-ray Structure Validation Report i
Full wwpdb X-ray Structure Validation Report i Feb 17, 2018 01:16 am GMT PDB ID : 1IFT Title : RICIN A-CHAIN (RECOMBINANT) Authors : Weston, S.A.; Tucker, A.D.; Thatcher, D.R.; Derbyshire, D.J.; Pauptit,
More informationFull wwpdb X-ray Structure Validation Report i
Full wwpdb X-ray Structure Validation Report i Mar 14, 2018 02:00 pm GMT PDB ID : 3RRQ Title : Crystal structure of the extracellular domain of human PD-1 Authors : Lazar-Molnar, E.; Ramagopal, U.A.; Nathenson,
More informationFull wwpdb X-ray Structure Validation Report i
Full wwpdb X-ray Structure Validation Report i Mar 10, 2018 01:44 am GMT PDB ID : 1MWP Title : N-TERMINAL DOMAIN OF THE AMYLOID PRECURSOR PROTEIN Authors : Rossjohn, J.; Cappai, R.; Feil, S.C.; Henry,
More informationFull wwpdb X-ray Structure Validation Report i
Full wwpdb X-ray Structure Validation Report i Jan 14, 2019 11:10 AM EST PDB ID : 6GYW Title : Crystal structure of DacA from Staphylococcus aureus Authors : Tosi, T.; Freemont, P.S.; Grundling, A. Deposited
More informationwwpdb X-ray Structure Validation Summary Report
wwpdb X-ray Structure Validation Summary Report io Jan 31, 2016 06:45 PM GMT PDB ID : 1CBS Title : CRYSTAL STRUCTURE OF CELLULAR RETINOIC-ACID-BINDING PROTEINS I AND II IN COMPLEX WITH ALL-TRANS-RETINOIC
More informationFull wwpdb X-ray Structure Validation Report i
Full wwpdb X-ray Structure Validation Report i Mar 8, 2018 08:34 pm GMT PDB ID : 1RUT Title : Complex of LMO4 LIM domains 1 and 2 with the ldb1 LID domain Authors : Deane, J.E.; Ryan, D.P.; Maher, M.J.;
More informationFull wwpdb X-ray Structure Validation Report i
Full wwpdb X-ray Structure Validation Report i Mar 7, 2018 09:30 am GMT PDB ID : 2VGF Title : HUMAN ERYTHROCYTE PYRUVATE KINASE: T384M mutant Authors : Valentini, G.; Chiarelli, L.R.; Fortin, R.; Dolzan,
More informationFull wwpdb/emdatabank EM Map/Model Validation Report i
Full wwpdb/emdatabank EM Map/Model Validation Report i Sep 25, 2018 07:01 PM EDT PDB ID : 6C0V EMDB ID: : EMD-7325 Title : Molecular structure of human P-glycoprotein in the ATP-bound, outwardfacing conformation
More informationFull wwpdb NMR Structure Validation Report i
Full wwpdb NMR Structure Validation Report i Feb 17, 2018 06:22 am GMT PDB ID : 141D Title : SOLUTION STRUCTURE OF A CONSERVED DNA SEQUENCE FROM THE HIV-1 GENOME: RESTRAINED MOLECULAR DYNAMICS SIMU- LATION
More informationFull wwpdb/emdatabank EM Map/Model Validation Report io
Full wwpdb/emdatabank EM Map/Model Validation Report io Apr 11, 218 7:1 PM EDT PDB ID : 6CV EMDB ID: : EMD-7631 Title : Cryo-electron microscopy structure of infectious bronchitis coronavirus spike protein
More informationFull wwpdb/emdatabank EM Map/Model Validation Report i
Full wwpdb/emdatabank EM Map/Model Validation Report i Feb 20, 2018 02:57 pm GMT PDB ID : 3ZYS EMDB ID: : EMD-1949 Title : Human dynamin 1 deltaprd polymer stabilized with GMPPCP Authors : Chappie, J.S.;
More informationFull wwpdb/emdatabank EM Map/Model Validation Report io
Full wwpdb/emdatabank EM Map/Model Validation Report io Apr 9, 218 2:5 PM EDT PDB ID : 6AUI EMDB ID: : EMD-76 Title : Human ribonucleotide reductase large subunit (alpha) with datp and CDP Authors : Brignole,
More informationFull wwpdb X-ray Structure Validation Report i
Full wwpdb X-ray Structure Validation Report i Feb 20, 2018 01:37 am GMT PDB ID : 1RU7 Title : 1934 Human H1 Hemagglutinin Authors : Skehel, J.J.; Gamblin, S.J.; Haire, L.F.; Russell, R.J.; Stevens, D.J.;
More informationFull wwpdb X-ray Structure Validation Report i
Full wwpdb X-ray Structure Validation Report i Mar 13, 2018 11:41 am GMT PDB ID : 1SMK Title : Mature and translocatable forms of glyoxysomal malate dehydrogenase have different activities and stabilities
More informationFull wwpdb X-ray Structure Validation Report i
Full wwpdb X-ray Structure Validation Report i Mar 14, 2018 02:38 pm GMT PDB ID : 4Z5R Title : Rontalizumab Fab bound to Interferon-a2 Authors : Eigenbrot, C.; Maurer, B.; Bosanac, I. Deposited on : 2015-04-02
More informationFull wwpdb/emdatabank EM Map/Model Validation Report i
Full wwpdb/emdatabank EM Map/Model Validation Report i Oct 9, 2018 11:26 AM EDT PDB ID : 5MLC EMDB ID: : EMD-3525 Title : Cryo-EM structure of the spinach chloroplast ribosome reveals the location of plastid-specific
More information1.b What are current best practices for selecting an initial target ligand atomic model(s) for structure refinement from X-ray diffraction data?!
1.b What are current best practices for selecting an initial target ligand atomic model(s) for structure refinement from X-ray diffraction data?! Visual analysis: Identification of ligand density from
More informationFull wwpdb X-ray Structure Validation Report
Full wwpdb X-ray Structure Validation Report io Apr 15, 2018 10:21 PM EDT PDB ID : 2W5J Title : Structure of the c14-rotor ring of the proton translocating chloroplast ATP synthase Authors : Vollmar, M.;
More informationElectronic Supplementary Information (ESI) for Chem. Commun. Unveiling the three- dimensional structure of the green pigment of nitrite- cured meat
Electronic Supplementary Information (ESI) for Chem. Commun. Unveiling the three- dimensional structure of the green pigment of nitrite- cured meat Jun Yi* and George B. Richter- Addo* Department of Chemistry
More informationThe structure of Aquifex aeolicus FtsH in the ADP-bound state reveals a C2-symmetric hexamer
Volume 71 (2015) Supporting information for article: The structure of Aquifex aeolicus FtsH in the ADP-bound state reveals a C2-symmetric hexamer Marina Vostrukhina, Alexander Popov, Elena Brunstein, Martin
More informationMultivariate Analyses of Quality Metrics for Crystal Structures in the PDB Archive
Article Multivariate Analyses of Quality Metrics for Crystal Structures in the PDB Archive Graphical Abstract Authors Chenghua Shao, Huanwang Yang, John D. Westbrook, Jasmine Y. Young, Christine Zardecki,
More informationProtein Data Bank Contents Guide: Atomic Coordinate Entry Format Description. Version 3.0, December 1, 2006 Updated to Version 3.
Protein Data Bank Contents Guide: Atomic Coordinate Entry Format Description Version 3.0, December 1, 2006 Updated to Version 3.01 March 30, 2007 1. Introduction The Protein Data Bank (PDB) is an archive
More informationTable S1. Overview of used PDZK1 constructs and their binding affinities to peptides. Related to figure 1.
Table S1. Overview of used PDZK1 constructs and their binding affinities to peptides. Related to figure 1. PDZK1 constru cts Amino acids MW [kda] KD [μm] PEPT2-CT- FITC KD [μm] NHE3-CT- FITC KD [μm] PDZK1-CT-
More informationA new generation of crystallographic validation tools for the Protein Data Bank
A new generation of crystallographic validation tools for the Protein Data Bank Randy J. Read 1,*, Paul D. Adams 2, W. Bryan Arendall III 3, Axel T. Brunger 4, Paul Emsley 5, Robbie P. Joosten 6,7, Gerard
More informationIgE binds asymmetrically to its B cell receptor CD23
Supplementary Information IgE binds asymmetrically to its B cell receptor CD23 Balvinder Dhaliwal 1*, Marie O. Y. Pang 2, Anthony H. Keeble 2,3, Louisa K. James 2,4, Hannah J. Gould 2, James M. McDonnell
More informationProtein structure analysis. Risto Laakso 10th January 2005
Protein structure analysis Risto Laakso risto.laakso@hut.fi 10th January 2005 1 1 Summary Various methods of protein structure analysis were examined. Two proteins, 1HLB (Sea cucumber hemoglobin) and 1HLM
More informationHelpful resources for all X ray lectures Crystallization http://www.hamptonresearch.com under tech support: crystal growth 101 literature Spacegroup tables http://img.chem.ucl.ac.uk/sgp/mainmenu.htm Crystallography
More informationHOMOLOGY MODELING. The sequence alignment and template structure are then used to produce a structural model of the target.
HOMOLOGY MODELING Homology modeling, also known as comparative modeling of protein refers to constructing an atomic-resolution model of the "target" protein from its amino acid sequence and an experimental
More informationSUPPLEMENTARY INFORMATION
doi:1.138/nature1737 Supplementary Table 1 variant Description FSEC - 2B12 a FSEC - 6A1 a K d (leucine) c Leucine uptake e K (wild-type like) K (Y18F) K (TS) K (TSY) K288A mutant, lipid facing side chain
More informationNature Structural and Molecular Biology: doi: /nsmb Supplementary Figure 1. Experimental approach for enhancement of unbiased Fo Fc maps.
Supplementary Figure 1 Experimental approach for enhancement of unbiased Fo Fc maps. a, c, Unbiased Fo-Fc maps of the Tth 70S post-catalysis complex at 2.55 Å resolution with (a) or without (c) bulk solvent
More informationX-ray Crystallography I. James Fraser Macromolecluar Interactions BP204
X-ray Crystallography I James Fraser Macromolecluar Interactions BP204 Key take-aways 1. X-ray crystallography results from an ensemble of Billions and Billions of molecules in the crystal 2. Models in
More informationHTCondor and macromolecular structure validation
HTCondor and macromolecular structure validation Vincent Chen John Markley/Eldon Ulrich, NMRFAM/BMRB, UW@Madison David & Jane Richardson, Duke University Macromolecules David S. Goodsell 1999 Two questions
More informationA New Generation of Crystallographic Validation Tools for the Protein Data Bank
Ways & Means A New Generation of Crystallographic Validation Tools for the Protein Data Bank Randy J. Read, 1, * Paul D. Adams, 2 W. Bryan Arendall, III, 3 Axel T. Brunger, 4 Paul Emsley, 5 Robbie P. Joosten,
More informationChapter 24. Stereochemistry and Validation of Macromolecular Structures. Alexander Wlodawer. Abstract. 1 Introduction
Chapter 24 Stereochemistry and Validation of Macromolecular Structures Abstract Macromolecular structure is governed by the strict rules of stereochemistry. Several approaches to the validation of the
More informationAutomated identification of functional dynamic contact networks from X-ray crystallography
1 Automated identification of functional dynamic contact networks from X-ray crystallography Henry van den Bedem, Gira Bhabha, Kun Yang, Peter E. Wright and James S. Fraser Supplementary Figure 1 Supplementary
More informationNitrogenase MoFe protein from Clostridium pasteurianum at 1.08 Å resolution: comparison with the Azotobacter vinelandii MoFe protein
Acta Cryst. (2015). D71, 274-282, doi:10.1107/s1399004714025243 Supporting information Volume 71 (2015) Supporting information for article: Nitrogenase MoFe protein from Clostridium pasteurianum at 1.08
More informationProtein Data Bank Contents Guide: Atomic Coordinate Entry Format Description. Version Document Published by the wwpdb
Protein Data Bank Contents Guide: Atomic Coordinate Entry Format Description Version 3.30 Document Published by the wwpdb This format complies with the PDB Exchange Dictionary (PDBx) http://mmcif.pdb.org/dictionaries/mmcif_pdbx.dic/index/index.html.
More informationTwinning in PDB and REFMAC. Garib N Murshudov Chemistry Department, University of York, UK
Twinning in PDB and REFMAC Garib N Murshudov Chemistry Department, University of York, UK Contents Crystal peculiarities Problem of twinning Occurrences of twinning in PDB Recognition of potential operators
More informationFull wwpdb/emdatabank EM Map/Model Validation Report i
Full wwpdb/emdatabank EM Map/Model Validation Report i Dec 8, 2018 02:45 PM EST PDB ID : 6MUT EMDB ID: : EMD-9255 Title : ryo-em structure of ternary sm-crrna-target RNA with anti-tag sequence complex
More informationActa Cryst. (2017). D73, doi: /s
Acta Cryst. (2017). D73, doi:10.1107/s2059798317010932 Supporting information Volume 73 (2017) Supporting information for article: Designing better diffracting crystals of biotin carboxyl carrier protein
More informationSUPPLEMENTARY INFORMATION. doi: /nature07461
Figure S1 Electrophysiology. a ph-activation of. Two-electrode voltage clamp recordings of Xenopus oocytes expressing in comparison to waterinjected oocytes. Currents were recorded at 40 mv. The ph of
More informationJoana Pereira Lamzin Group EMBL Hamburg, Germany. Small molecules How to identify and build them (with ARP/wARP)
Joana Pereira Lamzin Group EMBL Hamburg, Germany Small molecules How to identify and build them (with ARP/wARP) The task at hand To find ligand density and build it! Fitting a ligand We have: electron
More informationPAN-modular Structure of Parasite Sarcocystis muris Microneme Protein SML-2 at 1.95 Å Resolution and the Complex with 1-Thio-β-D-Galactose
Supplementary Material to the paper: PAN-modular Structure of Parasite Sarcocystis muris Microneme Protein SML-2 at 1.95 Å Resolution and the Complex with 1-Thio-β-D-Galactose Jürgen J. Müller, a Manfred
More informationPDBe TUTORIAL. PDBePISA (Protein Interfaces, Surfaces and Assemblies)
PDBe TUTORIAL PDBePISA (Protein Interfaces, Surfaces and Assemblies) http://pdbe.org/pisa/ This tutorial introduces the PDBePISA (PISA for short) service, which is a webbased interactive tool offered by
More information8. Strategies for Macromolecular Refinement
8. Strategies for Macromolecular Refinement SHELXL is designed to be easy to use and general for all space groups and uses a conventional structure-factor calculation rather than a FFT summation; the latter
More informationConformational Geometry of Peptides and Proteins:
Conformational Geometry of Peptides and Proteins: Before discussing secondary structure, it is important to appreciate the conformational plasticity of proteins. Each residue in a polypeptide has three
More informationReport of protein analysis
Report of protein analysis By the WHAT IF program 2010-09-19 1 Introduction what check is the name of the validation option in what if. It doesn t matter whether you use the what check program or the what
More informationGarib N Murshudov MRC-LMB, Cambridge
Garib N Murshudov MRC-LMB, Cambridge Contents Introduction AceDRG: two functions Validation of entries in the DB and derived data Generation of new ligand description Jligand for link description Conclusions
More informationTable 1. Crystallographic data collection, phasing and refinement statistics. Native Hg soaked Mn soaked 1 Mn soaked 2
Table 1. Crystallographic data collection, phasing and refinement statistics Native Hg soaked Mn soaked 1 Mn soaked 2 Data collection Space group P2 1 2 1 2 1 P2 1 2 1 2 1 P2 1 2 1 2 1 P2 1 2 1 2 1 Cell
More informationManipulating Ligands Using Coot. Paul Emsley May 2013
Manipulating Ligands Using Coot Paul Emsley May 2013 Ligand and Density... Ligand and Density... Ligand and Density... Protein-ligand complex models are often a result of subjective interpretation Scoring
More informationCrystals, X-rays and Proteins
Crystals, X-rays and Proteins Comprehensive Protein Crystallography Dennis Sherwood MA (Hons), MPhil, PhD Jon Cooper BA (Hons), PhD OXFORD UNIVERSITY PRESS Contents List of symbols xiv PART I FUNDAMENTALS
More informationCryo-EM data collection, refinement and validation statistics
1 Table S1 Cryo-EM data collection, refinement and validation statistics Data collection and processing CPSF-160 WDR33 (EMDB-7114) (PDB 6BM0) CPSF-160 WDR33 (EMDB-7113) (PDB 6BLY) CPSF-160 WDR33 CPSF-30
More informationSUPPLEMENTARY INFORMATION
doi:10.1038/nature11054 Supplementary Fig. 1 Sequence alignment of Na v Rh with NaChBac, Na v Ab, and eukaryotic Na v and Ca v homologs. Secondary structural elements of Na v Rh are indicated above the
More informationSUPPLEMENTARY INFORMATION
Supplementary materials Figure S1 Fusion protein of Sulfolobus solfataricus SRP54 and a signal peptide. a, Expression vector for the fusion protein. The signal peptide of yeast dipeptidyl aminopeptidase
More informationHomology Modeling (Comparative Structure Modeling) GBCB 5874: Problem Solving in GBCB
Homology Modeling (Comparative Structure Modeling) Aims of Structural Genomics High-throughput 3D structure determination and analysis To determine or predict the 3D structures of all the proteins encoded
More informationRanjit P. Bahadur Assistant Professor Department of Biotechnology Indian Institute of Technology Kharagpur, India. 1 st November, 2013
Hydration of protein-rna recognition sites Ranjit P. Bahadur Assistant Professor Department of Biotechnology Indian Institute of Technology Kharagpur, India 1 st November, 2013 Central Dogma of life DNA
More informationThe copper active site in CBM33 polysaccharide oxygenases
Supporting Information for: The copper active site in CBM33 polysaccharide oxygenases Glyn R. Hemsworth, Edward J. Taylor, Robbert Q. Kim, Rebecca C. Gregory, Sally J. Lewis, Johan P. Turkenburg, Alison
More informationElectron Density at various resolutions, and fitting a model as accurately as possible.
Section 9, Electron Density Maps 900 Electron Density at various resolutions, and fitting a model as accurately as possible. ρ xyz = (Vol) -1 h k l m hkl F hkl e iφ hkl e-i2π( hx + ky + lz ) Amplitude
More informationSupplementary Information
1 Supplementary Information Figure S1 The V=0.5 Harker section of an anomalous difference Patterson map calculated using diffraction data from the NNQQNY crystal at 1.3 Å resolution. The position of the
More informationQ1 current best prac2ce
Group- A Q1 current best prac2ce Star2ng from some common molecular representa2on with bond orders, configura2on on chiral centers (e.g. ChemDraw, SMILES) NEW! PDB should become resource for refinement
More informationVisualization of Macromolecular Structures
Visualization of Macromolecular Structures Present by: Qihang Li orig. author: O Donoghue, et al. Structural biology is rapidly accumulating a wealth of detailed information. Over 60,000 high-resolution
More informationSUPPLEMENTARY INFORMATION
Table of Contents Page Supplementary Table 1. Diffraction data collection statistics 2 Supplementary Table 2. Crystallographic refinement statistics 3 Supplementary Fig. 1. casic1mfc packing in the R3
More informationNMR, X-ray Diffraction, Protein Structure, and RasMol
NMR, X-ray Diffraction, Protein Structure, and RasMol Introduction So far we have been mostly concerned with the proteins themselves. The techniques (NMR or X-ray diffraction) used to determine a structure
More informationFW 1 CDR 1 FW 2 CDR 2
Supplementary Figure 1 Supplementary Figure 1: Interface of the E9:Fas structure. The two interfaces formed by V H and V L of E9 with Fas are shown in stereo. The Fas receptor is represented as a surface
More informationSupporting Information. UV-induced ligand exchange in MHC class I protein crystals
Supporting Information for the article entitled UV-induced ligand exchange in MHC class I protein crystals by Patrick H.N. Celie 1, Mireille Toebes 2, Boris Rodenko 3, Huib Ovaa 3, Anastassis Perrakis
More informationTools for Cryo-EM Map Fitting. Paul Emsley MRC Laboratory of Molecular Biology
Tools for Cryo-EM Map Fitting Paul Emsley MRC Laboratory of Molecular Biology April 2017 Cryo-EM model-building typically need to move more atoms that one does for crystallography the maps are lower resolution
More informationRamachandran Plot. 4ysz Phi (degrees) Plot statistics
B Ramachandran Plot ~b b 135 b ~b ~l l Psi (degrees) 5-5 a A ~a L - -135 SER HIS (F) 59 (G) SER (B) ~b b LYS ASP ASP 315 13 13 (A) (F) (B) LYS ALA ALA 315 173 (E) 173 (E)(A) ~p p ~b - -135 - -5 5 135 (degrees)
More informationSummary of Experimental Protein Structure Determination. Key Elements
Programme 8.00-8.20 Summary of last week s lecture and quiz 8.20-9.00 Structure validation 9.00-9.15 Break 9.15-11.00 Exercise: Structure validation tutorial 11.00-11.10 Break 11.10-11.40 Summary & discussion
More information*Corresponding Author *K. F.: *T. H.:
Theoretical Analysis of Activity Cliffs among Benzofuranone Class Pim1 Inhibitors Using the Fragment Molecular Orbital Method with Molecular Mechanics Poisson-Boltzmann Surface Area (FMO+MM-PBSA) Approach
More informationIntroduction to Comparative Protein Modeling. Chapter 4 Part I
Introduction to Comparative Protein Modeling Chapter 4 Part I 1 Information on Proteins Each modeling study depends on the quality of the known experimental data. Basis of the model Search in the literature
More informationRietveld Structure Refinement of Protein Powder Diffraction Data using GSAS
Rietveld Structure Refinement of Protein Powder Diffraction Data using GSAS Jon Wright ESRF, Grenoble, France Plan This is a users perspective Cover the protein specific aspects (assuming knowledge of
More informationSUPPLEMENTARY INFORMATION
www.nature.com/nature 1 Figure S1 Sequence alignment. a Structure based alignment of the plgic of E. chrysanthemi (ELIC), the acetylcholine binding protein from the snail Lymnea stagnalis (AchBP, PDB code
More informationReport of protein analysis
Report of protein analysis By the WHAT IF program 2010-09-19 1 Introduction what check is the name of the validation option in what if. It doesn t matter whether you use the what check program or the what
More informationSHELXC/D/E. Andrea Thorn
SHELXC/D/E Andrea Thorn What is experimental phasing? Experimental phasing is what you do if MR doesn t work. What is experimental phasing? Experimental phasing methods depend on intensity differences.
More informationTemplate Free Protein Structure Modeling Jianlin Cheng, PhD
Template Free Protein Structure Modeling Jianlin Cheng, PhD Associate Professor Computer Science Department Informatics Institute University of Missouri, Columbia 2013 Protein Energy Landscape & Free Sampling
More informationCRYSTALLOGRAPHY AND STORYTELLING WITH DATA. President, Association of Women in Science, Bethesda Chapter STEM Consultant
CRYSTALLOGRAPHY AND STORYTELLING WITH DATA President, Association of Women in Science, Bethesda Chapter STEM Consultant MY STORY Passion for Science BS Biology Major MS Biotechnology & Project in Bioinformatics
More informationMacromolecular Crystallography Part II
Molecular Biology Course 2010 Macromolecular Crystallography Part II University of Göttingen Dept. of Structural Chemistry November 2010 http://shelx.uni-ac.gwdg.de tg@shelx.uni-ac.gwdg.de Crystallography
More informationCks1 CDK1 CDK1 CDK1 CKS1. are ice- lobe. conserved. conserved
Cks1 d CKS1 Supplementary Figure 1 The -Cks1 crystal lattice. (a) Schematic of the - Cks1 crystal lattice. -Cks1 crystallizes in a lattice that contains c 4 copies of the t - Cks1 dimer in the crystallographic
More informationOrientational degeneracy in the presence of one alignment tensor.
Orientational degeneracy in the presence of one alignment tensor. Rotation about the x, y and z axes can be performed in the aligned mode of the program to examine the four degenerate orientations of two
More informationModel Mélange. Physical Models of Peptides and Proteins
Model Mélange Physical Models of Peptides and Proteins In the Model Mélange activity, you will visit four different stations each featuring a variety of different physical models of peptides or proteins.
More informationVisualizing and Discriminating Atom Intersections Within the Spiegel Visualization Framework
Visualizing and Discriminating Atom Intersections Within the Spiegel Visualization Framework Ian McIntosh May 19, 2006 Contents Abstract. 3 Overview 1.1 Spiegel. 3 1.2 Atom Intersections... 3 Intersections
More informationAnisotropy in macromolecular crystal structures. Andrea Thorn July 19 th, 2012
Anisotropy in macromolecular crystal structures Andrea Thorn July 19 th, 2012 Motivation Courtesy of M. Sawaya Motivation Crystal structures are inherently anisotropic. X-ray diffraction reflects this
More informationStabilizing the CH2 domain of an Antibody by Engineering in an Enhanced Aromatic Sequon
Stabilizing the CH2 domain of an Antibody by Engineering in an Enhanced Aromatic Sequon Wentao Chen,, Leopold Kong, Stephen Connelly, Julia M. Dendle,, Yu Liu,, Ian A. Wilson,#, Evan T. Powers, *, Jeffery
More informationActa Crystallographica Section F
Supporting information Acta Crystallographica Section F Volume 70 (2014) Supporting information for article: Chemical conversion of cisplatin and carboplatin with histidine in a model protein crystallised
More informationPhysiochemical Properties of Residues
Physiochemical Properties of Residues Various Sources C N Cα R Slide 1 Conformational Propensities Conformational Propensity is the frequency in which a residue adopts a given conformation (in a polypeptide)
More informationExperimental and Computational Mutagenesis to Investigate the. Positioning of a General Base within an Enzyme Active Site
Experimental and Computational Mutagenesis to Investigate the Positioning of a General Base within an Enzyme Active Site Jason P. Schwans, Philip Hanoian, Benjamin J. Lengerich, Fanny Sunden, Ana Gonzalez
More informationSupplemental Information. Molecular Basis of Spectral Diversity. in Near-Infrared Phytochrome-Based. Fluorescent Proteins
Chemistry & Biology, Volume 22 Supplemental Information Molecular Basis of Spectral Diversity in Near-Infrared Phytochrome-Based Fluorescent Proteins Daria M. Shcherbakova, Mikhail Baloban, Sergei Pletnev,
More informationProtein Structure Determination. Part 1 -- X-ray Crystallography
Protein Structure Determination Part 1 -- X-ray Crystallography Topics covering in this 1/2 course Crystal growth Diffraction theory Symmetry Solving phases using heavy atoms Solving phases using a model
More informationLS1a Fall 2014 Problem Set #2 Due Monday 10/6 at 6 pm in the drop boxes on the Science Center 2 nd Floor
LS1a Fall 2014 Problem Set #2 Due Monday 10/6 at 6 pm in the drop boxes on the Science Center 2 nd Floor Note: Adequate space is given for each answer. Questions that require a brief explanation should
More informationStructure factors again
Structure factors again Remember 1D, structure factor for order h F h = F h exp[iα h ] = I 01 ρ(x)exp[2πihx]dx Where x is fractional position along unit cell distance (repeating distance, origin arbitrary)
More information= (8) V = (8) Å 3 Z =4 Mo K radiation. Data collection. Refinement. R[F 2 >2(F 2 )] = wr(f 2 ) = S = reflections
organic compounds Acta Crystallographica Section E Structure Reports Online ISSN 1600-5368 1-(3-Amino-1H-inden-2-yl)ethanone Dong-Yue Hu and Zhi-Rong Qu* Ordered Matter Science Research Center, College
More informationThis is an author produced version of Privateer: : software for the conformational validation of carbohydrate structures.
This is an author produced version of Privateer: : software for the conformational validation of carbohydrate structures. White Rose Research Online URL for this paper: http://eprints.whiterose.ac.uk/95794/
More informationBioinformatics. Macromolecular structure
Bioinformatics Macromolecular structure Contents Determination of protein structure Structure databases Secondary structure elements (SSE) Tertiary structure Structure analysis Structure alignment Domain
More informationEnhancing Specificity in the Janus Kinases: A Study on the Thienopyridine. JAK2 Selective Mechanism Combined Molecular Dynamics Simulation
Electronic Supplementary Material (ESI) for Molecular BioSystems. This journal is The Royal Society of Chemistry 2015 Supporting Information Enhancing Specificity in the Janus Kinases: A Study on the Thienopyridine
More informationRamachandran and his Map
Ramachandran and his Map C Ramakrishnan Introduction C Ramakrishnan, retired professor from Molecular Biophysics Unit, Indian Institute of Science, Bangalore, has been associated with Professor G N Ramachandran
More information