Full wwpdb/emdatabank EM Map/Model Validation Report i

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1 Full wwpdb/emdatabank EM Map/Model Validation Report i Feb 20, :57 pm GMT PDB ID : 3ZYS EMDB ID: : EMD-1949 Title : Human dynamin 1 deltaprd polymer stabilized with GMPPCP Authors : Chappie, J.S.; Mears, J.A.; Fang, S.; Leonard, M.; Schmid, S.L.; Milligan, R.A.; Hinshaw, J.E.; Dyda, F. Deposited on : Resolution : Å(reported) Based on PDB ID : 2X2E, 1DYN, 3LJB This is a Full wwpdb/emdatabank EM Map/Model Validation Report for a publicly released PDB/EMDB 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. MolProbity : 4.02b-467 Percentile statistics : v01 (using entries in the PDB archive December 27th 2017) Ideal geometry (proteins) : Engh & Huber (2001) Ideal geometry (DNA, RNA) : Parkinson et. al. (1996) Validation Pipeline (wwpdb-vp) : trunk30686

2 Page 2 Full wwpdb/emdatabank EM Map/Model Validation Report 3ZYS 1 Overall quality at a glance i The following experimental techniques were used to determine the structure: ELECTRON MICROSCOPY The reported resolution of this entry is 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 EM structures (#Entries) (#Entries) Clashscore Ramachandran outliers Sidechain outliers The table below summarises the geometric issues observed across the polymeric chains. The red, orange, yellow and green segments on the 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% Mol Chain Length Quality of chain 1 A D B E C F 113

3 Page 3 Full wwpdb/emdatabank EM Map/Model Validation Report 3ZYS 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 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 protein called DYNAMIN-1. Mol Chain Residues Atoms AltConf Trace 1 A 330 Total C N O S D 330 Total C N O S There are 18 discrepancies between the modelled and reference sequences: Chain Residue Modelled Actual Comment Reference A linker UNP Q05193 A 322 HIS - linker UNP Q05193 A linker UNP Q05193 A linker UNP Q05193 A linker UNP Q05193 A linker UNP Q05193 A linker UNP Q05193 A linker UNP Q05193 A 744 variant UNP Q05193 D linker UNP Q05193 D 322 HIS - linker UNP Q05193 D linker UNP Q05193 D linker UNP Q05193 D linker UNP Q05193 D linker UNP Q05193 D linker UNP Q05193 D linker UNP Q05193 D 744 variant UNP Q05193 Molecule 2 is a protein called INTERFERON-INDUCED GTP-BINDING TEIN MX1. Mol Chain Residues Atoms AltConf Trace 2 B 211 Total C N O S

4 Page 4 Full wwpdb/emdatabank EM Map/Model Validation Report 3ZYS Mol Chain Residues Atoms AltConf Trace 2 E 219 Total C N O S Molecule 3 is a protein called DYNAMIN-1. Mol Chain Residues Atoms AltConf Trace 3 C 113 Total C N O S F 113 Total C N O S

5 Page 5 Full wwpdb/emdatabank EM Map/Model Validation Report 3ZYS 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 geometry. Residues are colorcoded 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. 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: DYNAMIN-1 Chain A: D726 E727 M728 Y732 H733 A734 L735 A738 I741 I745 T748 R228 Y231 I232 G233 V234 V235 K240 L252 E255 H262 P263 S264 M272 G273 T274 P275 Y276 L277 Q278 K279 V280 Q284 L285 I289 R290 R297 N298 K299 L300 Q301 L304 K309 E310 V311 HIS L84 R98 I101 E102 T105 D106 T111 L122 Y125 H128 V129 L130 N131 L132 T133 L134 P138 G139 M140 Q148 I156 M161 V164 L170 I171 L172 A177 G197 G202 T205 K206 L207 M210 D211 E212 L220 E221 N222 K223 L227 S5 M6 E7 D8 L9 I10 P11 L12 R15 L16 A19 I23 L29 D30 L31 I34 G39 Q40 S41 K44 S45 L48 E49 V52 G53 R54 L57 P58 R59 G60 S61 G62 I63 V64 T65 R66 R67 P68 L69 Q72 L73 V74 N75 F83 Molecule 1: DYNAMIN-1 Chain D: L277 L281 Q284 L285 I289 L293 R297 N298 K299 L300 Q301 L304 I307 E308 K309 E310 V311 HIS D726 E727 M728 Y732 A738 I741 I742 I745 T748 A186 V189 A190 G197 Q198 R199 T200 I201 I204 T205 K206 L207 E212 D218 V219 L220 L224 I232 G233 V234 V235 N236 R237 S238 Q239 K240 D241 I242 K245 K246 A250 A251 L252 E255 F258 F259 H262 P263 S264 Y265 D270 R271 M272 G273 T274 P275 Y276 E79 Y80 L84 K90 F91 T92 D93 F94 T109 K113 G114 I115 I120 N121 L122 R123 V124 Y125 L130 N131 L132 T133 L134 L137 P138 G139 M140 V145 G146 I156 L160 V164 L170 I171 L172 A173 V174 S175 P176 A177 N178 S179 D180 L181 A182 N183 S5 M6 E7 D8 L9 I10 P11 L12 V13 N14 R15 L16 A19 I23 L29 D30 L31 I34 A35 V36 V37 G38 G39 Q40 S41 A42 G43 K44 S45 S46 V47 L48 R54 R59 G60 S61 G62 I63 V64 T65 R66 R67 P68 L69 Q72 L73 V74 N75 A76 Molecule 2: INTERFERON-INDUCED GTP-BINDING TEIN MX1 Chain B: CYS TRP MET HIS CYS CYS

6 Page 6 Full wwpdb/emdatabank EM Map/Model Validation Report 3ZYS MET HIS MET HIS MET CYS HIS CYS HIS CYS HIS D367 E368 N369 E370 K371 M372 I376 V379 F382 L389 E398 I401 R402 L403 R406 L407 R408 I418 I428 L429 K432 K435 Y451 F454 I457 I462 L465 E466 A469 L473 H474 T475 V476 T477 D478 M479 V480 R481 L482 A483 F484 V487 F492 F495 L498 H499 R500 T501 A502 K503 S504 K505 I506 R510 Q513 L520 F525 E528 Q529 I530 V531 CYS TRP MET E576 I577 F578 L581 M582 A583 Y584 A588 R591 I592 S593 S594 H595 I596 P597 L598 I599 I600 Q601 F602 F603 M604 L612 A615 M616 L617 Q618 L619 L620 Q621 T625 Y626 L629 L630 T636 Molecule 2: INTERFERON-INDUCED GTP-BINDING TEIN MX1 Chain E: MET HIS CYS CYS CYS TRP MET HIS MET HIS MET CYS HIS CYS HIS CYS HIS E366 K371 M372 F373 F374 L375 I376 D377 K378 F382 I386 L389 I401 R402 L403 R406 L407 R408 W414 I417 F422 Q423 E424 G425 H426 K427 I428 R431 N438 F448 I462 L473 V476 T477 D478 M479 V480 R481 L482 A483 F484 F492 E493 E494 F495 F496 N497 L498 H499 R500 T501 A502 K503 S504 K505 I506 E507 D508 I509 R510 E514 G517 L520 I521 R522 L523 H524 F525 Q526 M527 E528 V531 Y532 CYS TRP S573 E576 Q579 M582 A583 Y584 H585 Q586 E587 A588 R591 I592 I596 I600 F603 M604 L605 Y608 L612 A615 M616 L617 Q618 L619

7 Page 7 Full wwpdb/emdatabank EM Map/Model Validation Report 3ZYS L620 K623 D624 T625 Y626 S627 W628 L629 L630 K631 E632 R633 Molecule 3: DYNAMIN-1 Chain C: E120 R121 V122 I10 L11 V12 I13 R14 K15 L18 T19 I20 I23 G24 I25 M26 K27 K31 E32 V36 K51 E52 K53 K54 N61 L62 K63 L64 R65 D66 V67 E68 K69 G70 F71 H76 I77 F78 R86 K90 D91 Y92 R93 Q94 L95 E96 L97 A98 C99 E104 V105 A115 Molecule 3: DYNAMIN-1 Chain F: I10 L11 R14 K15 I20 I23 G24 K27 K31 E32 Y33 W34 E50 K51 E52 K53 K54 Y55 M56 L57 N61 L62 K63 L64 R65 D66 V67 E68 K69 G70 F71 L80 F81 R86 N87 V88 Y89 Y92 R93 Q94 L95 C99 E104 V105 D106 S107 V122

8 Page 8 Full wwpdb/emdatabank EM Map/Model Validation Report 3ZYS 4 Experimental information i Property Value Source Reconstruction method HELICAL Depositor Imposed symmetry HELICAL, twist=not provided, rise=not Depositor provided Å, axial sym=not provided Number of segments used 4814 Depositor Resolution determination method Not provided Depositor CTF correction method INDIVIDUAL IMAGES USING ACE2 Depositor Microscope FEI TECNAI F20 Depositor Voltage (kv) 120 Depositor Electron dose (e /Å 2 ) 10 Depositor Minimum defocus (nm) 500 Depositor Maximum defocus (nm) 2000 Depositor Magnification Depositor Image detector GATAN ULTRASCAN 4000 (4k x 4k) Depositor

9 Page 9 Full wwpdb/emdatabank EM Map/Model Validation Report 3ZYS 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 >2 RMSZ # Z >2 1 A /2610 (0.0%) /3532 (0.8%) 1 D /2610 (0.2%) /3532 (0.9%) 2 B /1812 (0.1%) /2428 (0.7%) 2 E /1892 (0.8%) /2535 (4.1%) 3 C /966 (0.1%) /1298 (1.0%) 3 F /966 (0.3%) /1298 (1.4%) All All /10856 (0.2%) /14623 (1.4%) 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 A D B E C F 2 7 All All All (27) bond length outliers are listed below: Mol Chain Res Type Atoms Z Observed(Å) Ideal(Å) 2 E 495 C-O E 497 C-O D 61 CB-OG E 500 CD-NE E 496 C-O D 61 CA-CB E 496 CG-CD D 115 N-CA

10 Page 10 Full wwpdb/emdatabank EM Map/Model Validation Report 3ZYS Mol Chain Res Type Atoms Z Observed(Å) Ideal(Å) 1 A 61 N-CA D 245 CA-CB F 61 CA-CB E 500 CB-CG E 504 CB-OG E 498 C-N E 627 CB-OG E 500 C-O F 66 CA-CB E 628 TRP C-O B 603 CA-CB E 495 N-CA D 130 CA-CB E 500 N-CA F 53 N-CA E 579 CA-CB E 496 N-CA C 53 N-CA E 497 N-CA All (212) bond angle outliers are listed below: Mol Chain Res Type Atoms Z Observed( o ) Ideal( o ) 2 E 497 O-C-N E 500 NE-CZ-NH E 496 O-C-N E 495 O-C-N E 497 C-N-CA E 500 CD-NE-CZ E 498 O-C-N E 495 C-N-CA E 498 C-N-CA E 496 C-N-CA A 67 NE-CZ-NH E 496 CA-C-N A 129 CA-CB-CG E 498 CA-C-N B 408 NE-CZ-NH E 495 CA-C-N E 498 CA-CB-CG D 224 CB-CG-CD E 494 C-N-CA

11 Page 11 Full wwpdb/emdatabank EM Map/Model Validation Report 3ZYS Mol Chain Res Type Atoms Z Observed( o ) Ideal( o ) 2 E 500 NE-CZ-NH D 67 NE-CZ-NH E 625 CA-CB-CG E 500 CG-CD-NE E 497 CA-C-N E 532 CB-CG-CD B 603 N-CA-CB E 625 O-C-N E 579 N-CA-CB E 501 CA-CB-CG E 500 O-C-N D 114 C-N-CA E 498 CB-CG-CD B 604 MET N-CA-CB A 60 C-N-CA D 67 NE-CZ-NH F 61 CA-CB-CG E 497 CA-C-O E 527 MET CG-SD-CE E 499 HIS C-N-CA A 125 CB-CG-CD E 496 N-CA-C E 497 N-CA-C E 527 MET O-C-N E 496 CZ-CE2-CD E 576 CA-CB-CG E 499 HIS O-C-N F 50 CA-CB-CG E 500 CB-CG-CD E 500 NH1-CZ-NH E 527 MET CA-CB-CG A 61 N-CA-CB E 495 CB-CA-C E 532 CA-C-O E 628 TRP O-C-N E 505 CD-CE-NZ D 72 CB-CA-C E 631 CA-CB-CG E 633 NE-CZ-NH B 601 CA-CB-CG A 72 CB-CA-C D 61 CA-CB-OG

12 Page 12 Full wwpdb/emdatabank EM Map/Model Validation Report 3ZYS Mol Chain Res Type Atoms Z Observed( o ) Ideal( o ) 2 E 501 N-CA-CB A 131 C-N-CA A 212 CA-CB-CG E 498 N-CA-CB D 212 CA-CB-CG E 629 CA-C-N D 90 C-N-CA B 602 O-C-N E 499 HIS CB-CA-C F 66 CB-CG-OD A 125 CB-CG-CD D 130 N-CA-CB B 603 CA-C-O A 129 C-N-CA E 495 CB-CG-CD E 532 CB-CG-CD B 402 NE-CZ-NH E 631 CB-CG-CD A 73 N-CA-CB E 629 O-C-N E 438 CA-C-O E 626 N-CA-CB A 140 MET CA-CB-CG D 130 CA-CB-CG A 130 N-CA-CB E 495 CD1-CG-CD C 52 C-N-CA A 134 CB-CG-CD D 201 CG1-CB-CG E 527 MET CA-C-O E 496 CB-CA-C E 499 HIS CA-C-N F 66 N-CA-CB F 52 C-N-CA E 631 CG-CD-CE D 245 CB-CG-CD D 90 O-C-N E 628 TRP CZ3-CH2-CZ E 493 N-CA-CB A 130 CA-CB-CG A 59 O-C-N D 91 N-CA-CB

13 Page 13 Full wwpdb/emdatabank EM Map/Model Validation Report 3ZYS Mol Chain Res Type Atoms Z Observed( o ) Ideal( o ) 1 D 67 CD-NE-CZ B 602 C-N-CA E 500 N-CA-CB E 507 O-C-N D 131 C-N-CA E 576 N-CA-CB D 115 N-CA-CB C 69 C-N-CA B 621 CG-CD-OE E 633 N-CA-C F 61 CB-CG-OD C 26 MET N-CA-CB E 501 O-C-N E 626 CE1-CZ-CE F 61 CB-CA-C F 55 N-CA-CB D 272 MET C-N-CA F 53 N-CA-CB B 603 O-C-N D 123 NE-CZ-NH A 131 O-C-N F 61 CB-CG-ND E 626 CZ-CE2-CD E 497 CB-CA-C A 129 CA-C-N E 629 CB-CG-CD C 53 N-CA-CB F 93 C-N-CA A 223 CD-CE-NZ B 529 O-C-N A 67 NE-CZ-NH E 503 O-C-N E 498 CB-CG-CD A 125 N-CA-CB E 628 TRP CG-CD2-CE E 492 N-CA-CB A 221 OE1-CD-OE F 69 C-N-CA E 495 CG-CD1-CE C 25 C-N-CA E 503 CA-CB-CG E 626 CD1-CE1-CZ

14 Page 14 Full wwpdb/emdatabank EM Map/Model Validation Report 3ZYS Mol Chain Res Type Atoms Z Observed( o ) Ideal( o ) 2 E 502 N-CA-CB C 76 HIS N-CA-CB D 91 O-C-N E 527 MET N-CA-CB E 497 N-CA-CB E 494 O-C-N E 633 CG-CD-NE E 633 CD-NE-CZ C 93 C-N-CA A 228 NE-CZ-NH E 492 O-C-N B 617 C-N-CA A 73 CB-CG-CD A 67 CD-NE-CZ F 51 C-N-CA C 51 C-N-CA B 603 CB-CG-CD E 527 MET C-N-CA B 481 NE-CZ-NH E 495 CG-CD2-CE D 245 N-CA-CB E 500 CA-C-N A 130 CB-CA-C E 625 OG1-CB-CG C 52 N-CA-CB F 93 O-C-N D 201 CA-CB-CG E 502 O-C-N E 628 TRP CH2-CZ2-CE D 270 C-N-CA C 93 O-C-N E 626 CG-CD2-CE F 67 C-N-CA E 510 CD-NE-CZ D 178 C-N-CA E 386 CB-CG1-CD D 270 O-C-N D 61 N-CA-CB C 92 N-CA-C E 528 O-C-N E 502 C-N-CA E 417 CA-CB-CG

15 Page 15 Full wwpdb/emdatabank EM Map/Model Validation Report 3ZYS Mol Chain Res Type Atoms Z Observed( o ) Ideal( o ) 3 F 92 N-CA-C D 115 CA-CB-CG E 630 N-CA-C E 625 CA-C-O E 496 CB-CG-CD D 224 CB-CA-C E 417 CB-CG1-CD B 621 CG-CD-NE A 60 O-C-N F 52 N-CA-C A 272 MET C-N-CA D 224 N-CA-CB A 223 N-CA-CB B 601 N-CA-CB D 272 MET O-C-N E 496 CD1-CG-CD E 584 CB-CG-CD E 579 CA-CB-CG F 69 O-C-N D 130 CB-CA-C C 69 O-C-N E 386 CA-CB-CG C 67 C-N-CA E 500 C-N-CA E 507 C-N-CA All (18) chirality outliers are listed below: Mol Chain Res Type Atom 1 A 726 CA 2 B 435 CA 3 C 26 MET CA 3 C 52 CA 1 D 91 CA 1 D 92 CB,CA 2 E 495 CA 2 E 497 CA 2 E 500 CA 2 E 528 CA 2 E 573 CA 2 E 579 CA 2 E 625 CB

16 Page 16 Full wwpdb/emdatabank EM Map/Model Validation Report 3ZYS Mol Chain Res Type Atom 2 E 626 CA 2 E 633 CA 3 F 52 CA 3 F 55 CA All (75) planarity outliers are listed below: Mol Chain Res Type Group 1 A 105 Mainchain 1 A 130 Mainchain 1 A 132 Mainchain 1 A 177 Mainchain 1 A 197 Mainchain 1 A 206 Mainchain 1 A 221 Sidechain 1 A 228 Sidechain 1 A 231 Sidechain 1 A 290 Sidechain 1 A 41 Mainchain 1 A 5 Mainchain 1 A 59 Peptide 1 A 60 Peptide 1 A 67 Sidechain 1 A 7 Mainchain 1 A 72 Mainchain 1 A 728 MET Mainchain 2 B 369 Sidechain 2 B 402 Sidechain 2 B 408 Sidechain 2 B 492 Mainchain 2 B 595 HIS Sidechain 2 B 602 Sidechain 2 B 620 Mainchain 2 B 626 Sidechain 3 C 24 Mainchain 3 C 61 Mainchain 3 C 68 Mainchain 3 C 99 CYS Mainchain 1 D 113 Mainchain,Peptide 1 D 114 Mainchain 1 D 197 Mainchain 1 D 43 Mainchain

17 Page 17 Full wwpdb/emdatabank EM Map/Model Validation Report 3ZYS Mol Chain Res Type Group 1 D 62 Mainchain 1 D 7 Mainchain 1 D 72 Mainchain 1 D 726 Mainchain 1 D 90 Peptide 1 D 91 Mainchain 2 E 373 Sidechain 2 E 494 Mainchain,Peptide 2 E 495 Sidechain,Mainchain,Peptide 2 E 496 Sidechain,Mainchain,Peptide 2 E 497 Mainchain 2 E 498 Peptide 2 E 499 HIS Sidechain,Mainchain 2 E 502 Mainchain 2 E 532 Sidechain 2 E 585 HIS Sidechain 2 E 587 Sidechain 2 E 608 Sidechain 2 E 616 MET Mainchain 2 E 620 Mainchain 2 E 625 Mainchain 2 E 626 Sidechain,Mainchain 2 E 629 Mainchain,Peptide 2 E 632 Mainchain 2 E 633 Sidechain 3 F 24 Mainchain 3 F 55 Sidechain,Mainchain 3 F 61 Sidechain,Mainchain 3 F 68 Mainchain 3 F 69 Mainchain 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 A D B

18 Page 18 Full wwpdb/emdatabank EM Map/Model Validation Report 3ZYS Mol Chain Non-H H(model) H(added) Clashes Symm-Clashes 2 E C F All All 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 16. All (345) 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:309::CE 2:E:374::HD :D:309::CE 2:E:374::CD :D:726::HB3 2:E:633::N :D:726::OD1 2:E:632::HG :D:726::CG 2:E:632::CG :D:726::OD1 2:E:632::CG :D:726::HB3 2:E:633::CA :D:309::HE2 2:E:374::CD :D:726::OD2 2:E:632::HG :D:726::CB 2:E:633::N :A:311::HG13 2:B:370::CD :D:726::CG 2:E:632::HG :A:311::HG13 2:B:370::OE :D:726::HB3 2:E:633::HA :D:726::CA 2:E:633::H :D:309::HE3 2:E:374::HD :D:726::HA 2:E:632::H :D:726::CG 2:E:632::HG :D:309::HE2 2:E:374::CG :D:726::OD2 2:E:632::CG :E:375::HB2 2:E:630::HD :D:726::HA 2:E:632::N :A:311::CG1 2:B:370::OE :A:73::HD22 1:A:129::HG :D:310::OE2 2:E:632::OE :A:311::CG1 2:B:370::CD :D:727::HG3 2:E:631::HD :D:309::HE2 2:E:374::HB :D:309::HE2 2:E:374::CB :D:199::HB3 1:D:284::HG

19 Page 19 Full wwpdb/emdatabank EM Map/Model Validation Report 3ZYS Atom-1 Atom-2 Interatomic Clash distance (Å) overlap (Å) 2:B:506::HG12 2:B:612::HD :D:9::HD11 1:D:289::HD :D:309::NZ 2:E:374::CD :D:726::CB 2:E:633::H :D:42::HA 1:D:206::HE :A:34::HG12 1:A:170::HB :E:477::HG21 2:E:514::HG :A:207::HB2 1:A:235::HG :D:310::HB3 2:E:632::OE :D:16::HD21 1:D:293::HD :A:232::HD11 1:A:280::HG :A:31::HB3 1:A:132::HD :D:235::HB 1:D:255::HA :B:403::HD21 2:B:480::HG :D:29::HD23 1:D:289::HG :D:170::HD13 1:D:281::HB :D:84::HB2 1:D:121::HB :A:23::HG12 1:A:734::HB :B:501::HB 2:B:619::HD :D:138::HB2 1:D:156::HG :E:531::HG13 2:E:584::HB :A:138::HB2 1:A:156::HG :A:232::HG21 1:A:277::HB :D:201::HG23 1:D:232::HD :B:403::HA 2:B:406::HD :A:63::HG21 1:A:148::HE :D:727::HB2 2:E:631::HG :D:12::HD23 1:D:745::HA :D:63::HG23 1:D:66::HD :D:232::HG23 1:D:272:MET:HA :F:65::HB2 3:F:122::HA :D:310::OE2 2:E:374::CE :B:498::HG 2:B:629::HD :D:726::HA 2:E:633::H :D:13::HG13 1:D:29::HD :E:427::HE2 2:E:431::HD :A:177::HB1 1:A:210:MET:HG :B:473::HA 2:B:600::HG :C:10::HG13 3:C:11::H :B:588::HA 2:B:591::HH :B:418::HD13 2:B:465::HD

20 Page 20 Full wwpdb/emdatabank EM Map/Model Validation Report 3ZYS Atom-1 Atom-2 Interatomic Clash distance (Å) overlap (Å) 1:D:173::HB1 1:D:186::HB :D:181::HD11 1:D:204::HD :D:726::CB 2:E:633::HA :D:726::C 2:E:633::H :C:27::HE3 3:C:54::HE :F:10::HG13 3:F:11::H :D:59::HA 1:D:64::HG :D:109::HB 1:D:114::HA :A:29::HD23 1:A:289::HG :E:403::HD21 2:E:480::HG :F:14::HH12 3:F:107::HB :A:39::HA2 1:A:140:MET:HG :F:23::HD12 3:F:27::HD :A:16::HA 1:A:741::HG :F:62::HD13 3:F:80::HD :D:309::HE3 2:E:374::CD :D:39::HA3 1:D:176::HG :A:132::HD21 1:A:285::HD :E:371::HG3 2:E:630::HD :D:137::HD13 1:D:160::HB :D:727::CG 2:E:631::HD :B:505::HD2 2:B:615::HB :F:20::HD13 3:F:95::HD :D:726::CA 2:E:633::N :B:477::HG23 2:B:604:MET:HG :D:42::HB3 1:D:44::HG :D:61::HA 1:D:239::HE :D:726::CB 2:E:632::C :A:132::HD21 1:A:285::HD :B:371::HE3 2:B:630::HD :B:379::HG11 2:B:617::HD :D:310::HB3 2:E:632::CD :D:174::HG13 1:D:205::HG :B:462::HG21 2:B:528::HB :E:407::HD11 2:E:476::HG :A:16::HB2 1:A:745::HD :B:418::HG21 2:B:593::HB :C:10::HG13 3:C:11::N :F:71::N 3:F:71::HD :F:99:CYS:HB2 3:F:105::HG :B:389::HD11 2:B:483::HB

21 Page 21 Full wwpdb/emdatabank EM Map/Model Validation Report 3ZYS Atom-1 Atom-2 Interatomic Clash distance (Å) overlap (Å) 3:F:10::HG13 3:F:11::N :D:23::HD11 1:D:738::HB :D:140:MET:HG3 1:D:160::HD :B:498::HD22 2:B:619::HD :F:99:CYS:HB3 3:F:104::HB :D:246::HE3 1:D:250::HB :A:48::HD22 1:A:134::HD :C:71::CD1 3:C:71::N :C:71::HD1 3:C:71::N :D:310::CB 2:E:632::OE :D:297::NH2 1:D:298::HB :F:71::N 3:F:71::CD :D:255::HG3 1:D:259::HE :A:10::HG12 1:A:130::HD :A:297::NH2 1:A:298::HB :A:19::HB2 1:A:741::HG :B:429::HB2 2:B:457::HD :E:372:MET:HG3 2:E:376::HD :C:15::HE2 3:C:36::HG :D:76::HB3 1:D:125::HB :A:304::HD13 1:A:732::HA :D:170::HD22 1:D:281::HD :E:505::HD3 2:E:615::HB :D:727::HG3 2:E:631::CD :D:130::HD23 1:D:132::HG :E:477::HG22 2:E:604:MET:HG :D:310::CB 2:E:632::CD :D:297::HB2 1:D:742::HG :B:451::HE1 2:B:581::HD :D:36::HG23 1:D:172::HB :E:623::HA 2:E:626::CD :A:161:MET:HA 1:A:164::HG :B:429::HD11 2:B:454::HB :D:19::HB2 1:D:741::HG :A:205::HA 1:A:234::HG :B:429::HG 2:B:578::CE :B:401::HD12 2:B:402::H :E:521::HG23 2:E:596::HD :A:132::HD11 1:A:285::HD :D:40::HA 1:D:139::HA :E:389::HD13 2:E:484::CD

22 Page 22 Full wwpdb/emdatabank EM Map/Model Validation Report 3ZYS Atom-1 Atom-2 Interatomic Clash distance (Å) overlap (Å) 2:B:398::N 2:B:398::OE :E:424::HG2 2:E:428::HD :F:66::H 3:F:122::HG :D:201::HG21 1:D:277::HD :D:80::HB3 1:D:92::HG :C:13::HD12 3:C:115::HB :A:235::H 1:A:255::HG :D:310::OE2 2:E:374::HE :F:69::H 3:F:69::HE :D:15::HG3 1:D:15::HH :D:726::OD1 2:E:632::HG :A:15::HH11 1:A:15::HG :A:170::HD21 1:A:284::HE :C:99:CYS:HB3 3:C:104::HB :D:310::HG2 2:E:630::O :D:10::HG12 1:D:130::HD :E:531::HA 2:E:584::CD :E:403::HD23 2:E:605::HD :A:45::HB2 1:A:59::HG :B:531::HA 2:B:584::CZ :A:16::HD22 1:A:745::HD :D:134::N 1:D:134::HD :F:54::O 3:F:55::HB :A:58::HG3 1:A:98::HG :E:378::HB3 2:E:492::HE :C:18::HD13 3:C:97::HD :D:205::HG22 1:D:234::HG :D:309::CE 2:E:374::HB :E:426:HIS:HA 2:E:582:MET:CE :D:218::HB3 1:D:224::HB :D:220::HD13 1:D:265::CE :B:406::HH11 2:B:406::HG :D:727::C 2:E:633::HG :D:304::HD11 1:D:732::CD :C:69::HE3 3:C:69::H :A:304::HB2 1:A:735::CD :A:58::HA 1:A:98::HD :D:207::HB3 1:D:258::CE :D:309::HB3 1:D:309::NZ :D:69::HD12 1:D:120::HB :A:170::HD21 1:A:284::HG

23 Page 23 Full wwpdb/emdatabank EM Map/Model Validation Report 3ZYS Atom-1 Atom-2 Interatomic Clash distance (Å) overlap (Å) 2:B:495::HB3 2:B:498::HB :E:528::HG2 2:E:591::NH :A:29::HD12 1:A:29::N :A:221::HB3 1:A:223::HE :A:12::HD23 1:A:745::HA :B:407::HD11 2:B:476::HG :C:54::HB3 3:C:90::NZ :A:63::HD13 1:A:148::NE :B:513::HB2 2:B:604:MET:CE :A:309::HB3 1:A:309::NZ :F:63::HB3 3:F:81::CZ :A:106::HB3 1:A:111::HG :D:23::HD11 1:D:738::CB :A:67::HD3 1:A:105::HA :D:37::HG11 1:D:164::HG :D:29::HD12 1:D:29::N :B:599::HG23 2:B:603::CD :E:403::HD11 2:E:480::HG :A:311::HA 1:A:726::N :E:625::HA 2:E:628:TRP:HB :D:113::HG3 1:D:146::HA :A:52::HG22 1:A:73::HD :B:429::HG 2:B:578::HE :D:726::OD1 2:E:632::CD :D:36::HG23 1:D:172::CB :A:23::HD11 1:A:738::HB :E:425::HA2 2:E:428::HD :A:10::HG12 1:A:130::CD :A:9::HD21 1:A:289::HD :B:499:HIS:NE2 2:B:503::HE :D:59::HA 1:D:64::CG :A:6:MET:SD 1:A:279::HA :D:40::HE22 1:D:145::HG :A:227::HD22 1:A:231::CZ :A:49::HB3 1:A:57::HD :C:23::HD12 3:C:27::HD :F:71::H 3:F:71::HD :D:190::HB1 1:D:200::CG :E:425::HA3 2:E:585:HIS:CE :D:34::HG12 1:D:170::HB :D:205::HG22 1:D:234::CG

24 Page 24 Full wwpdb/emdatabank EM Map/Model Validation Report 3ZYS Atom-1 Atom-2 Interatomic Clash distance (Å) overlap (Å) 1:A:12::CD2 1:A:745::HA :E:372:MET:CG 2:E:376::HD :D:232::HG12 1:D:276::HD :E:403::CD2 2:E:605::HD :D:180::HB2 1:D:183::ND :E:588::HA 2:E:591::NH :D:36::HB 1:D:48::HG :B:466::HG3 2:B:525::CD :B:505::CD 2:B:615::HB :D:304::HD11 1:D:732::HD :E:473::HD12 2:E:600::HG :A:220::HD13 1:A:272:MET:SD :E:473::HA 2:E:600::HG :D:79::HB3 1:D:94::CZ :F:57::CD2 3:F:62::HD :A:63::HD13 1:A:148::HE :A:235::HB 1:A:255::HA :B:625::O 2:B:625::HG :E:532::HA 2:E:584::HA :D:171::HD13 1:D:189::HG :F:23::HG23 3:F:27::HD :C:31::HG2 3:C:32::H :D:140:MET:CG 1:D:160::HD :E:506::HG13 2:E:612::HD :A:23::CD1 1:A:738::HB :A:83::CD2 1:A:122::HD :A:299::HD3 1:A:299::C :D:727::N 2:E:633::HG :E:517::HA2 2:E:603::CD :B:372:MET:HG2 2:B:376::HD :B:389::HD23 2:B:484::HD :C:54::HE3 3:C:90::HZ :D:72::HE22 1:D:74::HG :B:429::HD23 2:B:582:MET:SD :B:469::HB1 2:B:596::HG :B:520::HB3 2:B:599::HD :B:451::CE1 2:B:581::HD :E:422::HE1 2:E:586::HA :A:83::HZ 1:A:101::HG :D:12::HD23 1:D:745::HG :D:262:HIS:CE1 1:D:264::HB

25 Page 25 Full wwpdb/emdatabank EM Map/Model Validation Report 3ZYS Atom-1 Atom-2 Interatomic Clash distance (Å) overlap (Å) 3:F:31::HG2 3:F:32::H :C:20::CG2 3:C:23::HG :C:71::HD1 3:C:71::H :A:202::HA3 1:A:231::CD :C:92::O 3:C:93::HB :E:406::NH2 2:E:479:MET:HG :E:509::HG22 2:E:608::CD :D:726::HB3 2:E:633::CB :F:15::HB3 3:F:34:TRP:CZ :A:207::HA 1:A:207::HD :A:72::HE22 1:A:74::HG :D:299::HD3 1:D:299::C :F:92::O 3:F:93::HB :A:83::CE2 1:A:122::HD :C:54::HB3 3:C:90::HZ :F:20::CG2 3:F:23::HG :D:137::HD13 1:D:160::CB :A:66::NH2 1:A:102::HG :B:389::HD23 2:B:484::CD :E:520::HG 2:E:603::CZ :A:44::HE3 1:A:139::HA :E:498::HD13 2:E:629::HD :A:262:HIS:HA 1:A:263::HD :A:274::HB 1:A:275::HD :A:60::HA2 1:A:64::HG :D:310::O 2:E:630::O :D:727::HB2 2:E:631::HD :A:311::HG13 2:B:370::OE :B:382::CD2 2:B:487::HG :D:190::HB1 1:D:200::HG :D:59::HB3 1:D:242::HG :A:48::HA 1:A:48::HD :B:481::HG3 2:B:510::HH :E:631::HD2 2:E:633::NE :E:524:HIS:HA 2:E:527:MET:HG :E:498::CD1 2:E:629::HD :D:310::O 2:E:630::C :D:727::CB 2:E:631::HD :C:78::CD1 3:C:105::HG :D:174::HG13 1:D:205::CG :D:63::CG2 1:D:113::HA

26 Page 26 Full wwpdb/emdatabank EM Map/Model Validation Report 3ZYS Atom-1 Atom-2 Interatomic Clash distance (Å) overlap (Å) 1:D:307::HG23 1:D:726::N :A:262:HIS:CE1 1:A:264::HB :C:65::HB2 3:C:122::HG :D:79::HB3 1:D:94::HZ :F:20::CD1 3:F:95::HD :D:274::HB 1:D:275::HD :D:232::HG12 1:D:276::CD :E:462::HG23 2:E:592::HD :D:728:MET:N 2:E:633::HG :D:726::HA 2:E:633::N :A:177::CB 1:A:210:MET:HG :A:297::HH22 1:A:298::HB :F:88::HG13 3:F:89::HD :A:138::HB2 1:A:156::CG :B:469::CB 2:B:596::HG :B:506::HG13 2:B:612::HD :E:414:TRP:NE1 2:E:596::HB :E:523::HD12 2:E:526::HE :B:428::HG22 2:B:457::HD :B:473::HA 2:B:600::CG :E:401::CG2 2:E:406::HG :B:595:HIS:HE1 2:B:598::HD :E:509::HG22 2:E:608::HD :D:297::HH22 1:D:298::HB :D:12::HB3 1:D:745::HG :D:63::HG22 1:D:113::HA :E:382::HZ 2:E:612::HD :D:46::HB3 1:D:237::HH There are no symmetry-related clashes. 5.3 Torsion angles i Protein backbone i In the following table, the Percentiles column shows the percent Ramachandran outliers of the chain as a percentile score with respect to all PDB entries followed by that with respect to all EM entries. The Analysed column shows the number of residues for which the backbone conformation was analysed, and the total number of residues.

27 Page 27 Full wwpdb/emdatabank EM Map/Model Validation Report 3ZYS Mol Chain Analysed Favoured Allowed Outliers Percentiles 1 A 326/353 (92%) 315 (97%) 11 (3%) D 326/353 (92%) 314 (96%) 9 (3%) 3 (1%) B 205/662 (31%) 197 (96%) 7 (3%) 1 (0%) E 213/662 (32%) 198 (93%) 10 (5%) 5 (2%) C 111/113 (98%) 94 (85%) 13 (12%) 4 (4%) F 111/113 (98%) 95 (86%) 13 (12%) 3 (3%) 5 38 All All 1292/2256 (57%) 1213 (94%) 63 (5%) 16 (1%) All (16) Ramachandran outliers are listed below: Mol Chain Res Type 3 C 26 MET 3 C 68 1 D 91 1 D 92 1 D E E 499 HIS 2 E E F 68 2 B 604 MET 2 E C 69 3 C F 55 3 F Protein sidechains i In the following table, the Percentiles column shows the percent sidechain outliers of the chain as a percentile score with respect to all PDB entries followed by that with respect to all EM entries. The Analysed column shows the number of residues for which the sidechain conformation was analysed, and the total number of residues. Mol Chain Analysed Rotameric Outliers Percentiles 1 A 288/309 (93%) 268 (93%) 20 (7%) D 288/309 (93%) 269 (93%) 19 (7%) 18 49

28 Page 28 Full wwpdb/emdatabank EM Map/Model Validation Report 3ZYS Mol Chain Analysed Rotameric Outliers Percentiles 2 B 196/588 (33%) 177 (90%) 19 (10%) E 204/588 (35%) 189 (93%) 15 (7%) C 102/102 (100%) 94 (92%) 8 (8%) F 102/102 (100%) 92 (90%) 10 (10%) 9 32 All All 1180/1998 (59%) 1089 (92%) 91 (8%) All (91) residues with a non-rotameric sidechain are listed below: Mol Chain Res Type 1 A 31 1 A 48 1 A 54 1 A 69 1 A 73 1 A 75 1 A 84 1 A A 128 HIS 1 A A A 140 MET 1 A A A A A A A A B B B B B B B B 479 MET 2 B B B B 503

29 Page 29 Full wwpdb/emdatabank EM Map/Model Validation Report 3ZYS Mol Chain Res Type 2 B B B B B 604 MET 2 B B C 26 MET 3 C 52 3 C 63 3 C 69 3 C 71 3 C 76 HIS 3 C 86 3 C 95 1 D 31 1 D 48 1 D 54 1 D 61 1 D 69 1 D 75 1 D 84 1 D D D D D D D D D D D D E E E E E E E E 520

30 Page 30 Full wwpdb/emdatabank EM Map/Model Validation Report 3ZYS Mol Chain Res Type 2 E 527 MET 2 E E E E E E F 50 3 F 52 3 F 55 3 F 61 3 F 63 3 F 66 3 F 69 3 F 71 3 F 86 3 F 95 Some sidechains can be flipped to improve hydrogen bonding and reduce clashes. All (23) such sidechains are listed below: Mol Chain Res Type 1 A 33 1 A 75 1 A 85 HIS 1 A A A A A A A B B B B 595 HIS 3 C 94 1 D 75 1 D 85 HIS 1 D D D D 301

31 Page 31 Full wwpdb/emdatabank EM Map/Model Validation Report 3ZYS Mol Chain Res Type 1 D E 499 HIS RNA i There are no RNA molecules in this entry. 5.4 Non-standard residues in protein, DNA, RNA chains i There are no non-standard protein/dna/rna residues in this entry. 5.5 Carbohydrates i There are no carbohydrates in this entry. 5.6 Ligand geometry i There are no ligands in this entry. 5.7 Other polymers i There are no such residues in this entry. 5.8 Polymer linkage issues i The following chains have linkage breaks: Mol Chain Number of breaks 2 E 1 All chain breaks are listed below: Model Chain Residue-1 Atom-1 Residue-2 Atom-2 Distance (Å) 1 E 498: C 499:HIS N 1.19