Full wwpdb/emdatabank EM Map/Model Validation Report io

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1 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 Authors : Shang, J.; Zheng, Y.; Yang, Y.; Liu, C.; Geng, Q.; Luo, C.; Zhang, W.; Li, F. Deposited on : Resolution : 3.93 Å(reported) 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 specic help available everywhere you see the io symbol. MolProbity : 4.2b-467 Mogul : (15768), CSD as539be (218) Percentile statistics : v1 (using entries in the PDB archive December 27th 217) Ideal geometry (proteins) : Engh & Huber (21) Ideal geometry (DNA, RNA) : Parkinson et. al. (1996) Validation Pipeline (wwpdb-vp) : rb-23121

2 Page 2 Full wwpdb/emdatabank EM Map/Model Validation Report 6CV 1 Overall quality at a glance io The following experimental techniques were used to determine the structure: ELECTRON MICROSCOPY The reported resolution of this entry is 3.93 Å. Percentile scores (ranging between -1) 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 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 B C 115

3 Page 3 Full wwpdb/emdatabank EM Map/Model Validation Report 6CV 2 Entry composition io There are 2 unique types of molecules in this entry. The entry contains atoms, of which are hydrogens and 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. ˆ Molecule 1 is a protein called Spike glycoprotein. Mol Chain Residues Atoms AltConf Trace 1 A 993 S B 993 S C 993 S There are 153 discrepancies between the modelled and reference sequences: Chain Residue Modelled Actual Comment Reference A 126 conict UNP F4MIW6 A 823 conict UNP F4MIW6 A 829 conict UNP F4MIW6 A 849 VAL conict UNP F4MIW6 A 177 VAL - insertion UNP F4MIW6 A insertion UNP F4MIW6 A insertion UNP F4MIW6 A 18 - insertion UNP F4MIW6 A 181 GLN expression tag UNP F4MIW6 A 182 expression tag UNP F4MIW6 A insertion UNP F4MIW6 A 184 expression tag UNP F4MIW6 A insertion UNP F4MIW6 A insertion UNP F4MIW6 A 187 expression tag UNP F4MIW6 A 188 expression tag UNP F4MIW6 A 189 expression tag UNP F4MIW6 A 19 expression tag UNP F4MIW6 A expression tag UNP F4MIW6 A expression tag UNP F4MIW6 A expression tag UNP F4MIW6 A 194 TYR - expression tag UNP F4MIW6 A expression tag UNP F4MIW6 A expression tag UNP F4MIW6

4 Page 4 Full wwpdb/emdatabank EM Map/Model Validation Report 6CV Chain Residue Modelled Actual Comment Reference A expression tag UNP F4MIW6 A expression tag UNP F4MIW6 A expression tag UNP F4MIW6 A 11 - expression tag UNP F4MIW6 A 111 ALA - expression tag UNP F4MIW6 A 112 ARG - expression tag UNP F4MIW6 A expression tag UNP F4MIW6 A expression tag UNP F4MIW6 A expression tag UNP F4MIW6 A expression tag UNP F4MIW6 A expression tag UNP F4MIW6 A expression tag UNP F4MIW6 A expression tag UNP F4MIW6 A expression tag UNP F4MIW6 A expression tag UNP F4MIW6 A expression tag UNP F4MIW6 A expression tag UNP F4MIW6 A expression tag UNP F4MIW6 A expression tag UNP F4MIW6 A expression tag UNP F4MIW6 A expression tag UNP F4MIW6 A expression tag UNP F4MIW6 A expression tag UNP F4MIW6 A expression tag UNP F4MIW6 A expression tag UNP F4MIW6 A expression tag UNP F4MIW6 A expression tag UNP F4MIW6 B 126 conict UNP F4MIW6 B 823 conict UNP F4MIW6 B 829 conict UNP F4MIW6 B 849 VAL conict UNP F4MIW6 B 177 VAL - insertion UNP F4MIW6 B insertion UNP F4MIW6 B insertion UNP F4MIW6 B 18 - insertion UNP F4MIW6 B 181 GLN expression tag UNP F4MIW6 B 182 expression tag UNP F4MIW6 B insertion UNP F4MIW6 B 184 expression tag UNP F4MIW6 B insertion UNP F4MIW6 B insertion UNP F4MIW6 B 187 expression tag UNP F4MIW6

5 Page 5 Full wwpdb/emdatabank EM Map/Model Validation Report 6CV Chain Residue Modelled Actual Comment Reference B 188 expression tag UNP F4MIW6 B 189 expression tag UNP F4MIW6 B 19 expression tag UNP F4MIW6 B expression tag UNP F4MIW6 B expression tag UNP F4MIW6 B expression tag UNP F4MIW6 B 194 TYR - expression tag UNP F4MIW6 B expression tag UNP F4MIW6 B expression tag UNP F4MIW6 B expression tag UNP F4MIW6 B expression tag UNP F4MIW6 B expression tag UNP F4MIW6 B 11 - expression tag UNP F4MIW6 B 111 ALA - expression tag UNP F4MIW6 B 112 ARG - expression tag UNP F4MIW6 B expression tag UNP F4MIW6 B expression tag UNP F4MIW6 B expression tag UNP F4MIW6 B expression tag UNP F4MIW6 B expression tag UNP F4MIW6 B expression tag UNP F4MIW6 B expression tag UNP F4MIW6 B expression tag UNP F4MIW6 B expression tag UNP F4MIW6 B expression tag UNP F4MIW6 B expression tag UNP F4MIW6 B expression tag UNP F4MIW6 B expression tag UNP F4MIW6 B expression tag UNP F4MIW6 B expression tag UNP F4MIW6 B expression tag UNP F4MIW6 B expression tag UNP F4MIW6 B expression tag UNP F4MIW6 B expression tag UNP F4MIW6 B expression tag UNP F4MIW6 B expression tag UNP F4MIW6 C 126 conict UNP F4MIW6 C 823 conict UNP F4MIW6 C 829 conict UNP F4MIW6 C 849 VAL conict UNP F4MIW6 C 177 VAL - insertion UNP F4MIW6 C insertion UNP F4MIW6

6 Page 6 Full wwpdb/emdatabank EM Map/Model Validation Report 6CV Chain Residue Modelled Actual Comment Reference C insertion UNP F4MIW6 C 18 - insertion UNP F4MIW6 C 181 GLN expression tag UNP F4MIW6 C 182 expression tag UNP F4MIW6 C insertion UNP F4MIW6 C 184 expression tag UNP F4MIW6 C insertion UNP F4MIW6 C insertion UNP F4MIW6 C 187 expression tag UNP F4MIW6 C 188 expression tag UNP F4MIW6 C 189 expression tag UNP F4MIW6 C 19 expression tag UNP F4MIW6 C expression tag UNP F4MIW6 C expression tag UNP F4MIW6 C expression tag UNP F4MIW6 C 194 TYR - expression tag UNP F4MIW6 C expression tag UNP F4MIW6 C expression tag UNP F4MIW6 C expression tag UNP F4MIW6 C expression tag UNP F4MIW6 C expression tag UNP F4MIW6 C 11 - expression tag UNP F4MIW6 C 111 ALA - expression tag UNP F4MIW6 C 112 ARG - expression tag UNP F4MIW6 C expression tag UNP F4MIW6 C expression tag UNP F4MIW6 C expression tag UNP F4MIW6 C expression tag UNP F4MIW6 C expression tag UNP F4MIW6 C expression tag UNP F4MIW6 C expression tag UNP F4MIW6 C expression tag UNP F4MIW6 C expression tag UNP F4MIW6 C expression tag UNP F4MIW6 C expression tag UNP F4MIW6 C expression tag UNP F4MIW6 C expression tag UNP F4MIW6 C expression tag UNP F4MIW6 C expression tag UNP F4MIW6 C expression tag UNP F4MIW6 C expression tag UNP F4MIW6 C expression tag UNP F4MIW6

7 Page 7 Full wwpdb/emdatabank EM Map/Model Validation Report 6CV Chain Residue Modelled Actual Comment Reference C expression tag UNP F4MIW6 C expression tag UNP F4MIW6 C expression tag UNP F4MIW6 ˆ Molecule 2 is N-ACETYL-D-COSAMINE (three-letter code: NAG) (formula: C 8 H 15 NO 6 ). Mol Chain Residues Atoms AltConf

8 Page 8 Full wwpdb/emdatabank EM Map/Model Validation Report 6CV Mol Chain Residues Atoms AltConf

9 Page 9 Full wwpdb/emdatabank EM Map/Model Validation Report 6CV Mol Chain Residues Atoms AltConf

10 Page 1 Full wwpdb/emdatabank EM Map/Model Validation Report 6CV Mol Chain Residues Atoms AltConf

11 Page 11 Full wwpdb/emdatabank EM Map/Model Validation Report 6CV Mol Chain Residues Atoms AltConf

12 Page 12 Full wwpdb/emdatabank EM Map/Model Validation Report 6CV 3 Residue-property plots io These plots are drawn for all protein, RNA and DNA chains in the entry. The rst 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 =, 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: Spike glycoprotein Chain A: VAL GLN TYR ALA ARG V113 N114 K115 T119 V122 PHE PHE TRP TRP THR PRO PHE PHE TYR THR VAL PRO ARG GLN VAL GLN I85 Q856 V866 R89 Q894 R895 Q9 Q99 R912 C916 G917 R92 L923 T924 I925 A929 G932 I933 V934 H937 F938 S939 Y94 T941 K957 Q963 V967 P968 R972 F975 I984 D988 I995 D999 I1 V11 T61 R62 M63 C632 I635 N64 E646 E649 K658 P659 L667 L68 P684 V71 VAL PRO THR A711 Y712 K713 L72 K724 L738 Q747 I763 I769 P77 L775 R778 I784 A83 T833 N261 T265 N276 N283 N33 F331 L34 W341 F342 L345 I349 A35 Y351 G352 P353 V399 K43 R48 T449 L458 A459 D46 A461 G462 L463 Y485 F498 V56 G57 I58 S517 N522 I526 R537 Y551 G56 L57 ALA Y21 Y28 Y29 A33 F34 R35 A46 V5 I7 A1 H11 T17 T18 V19 K116 T123 V133 K137 K156 S157 N162 N163 L164 V167 N17 V174 V188 V2 E23 F21 V211 A215 Q216 L229 N247 Molecule 1: Spike glycoprotein Chain B: K115 T119 V122 PHE PHE TRP TRP THR PRO PHE PHE TYR THR VAL PRO ARG GLN VAL GLN VAL T833 I85 Q856 V866 R895 Q9 Q99 R912 C916 G917 R92 L923 T924 I925 A929 G932 I933 V934 H937 F938 S939 Y94 T941 K957 Q963 V967 P968 R972 F975 I984 D988 I995 D999 I1 V11 V113 N114 T61 R62 M63 C632 I635 N64 E646 E649 K658 P659 L667 L68 P684 V71 VAL PRO THR A711 Y712 K713 L72 K724 L738 P739 P74 Q747 I763 I769 P77 L775 R778 I784 A83 N247 N276 N283 N33 F331 F342 L345 I349 A35 Y351 G352 P353 V399 K43 R48 T449 D46 A461 G462 L463 Y485 C491 E492 F498 V56 G57 I58 S517 N522 I526 K527 I528 R537 Y551 G56 L57 ALA Y21 Y28 Y29 A33 F34 R35 A46 V5 I7 A1 H11 T17 T18 V19 K116 T123 V133 K137 Y143 K156 S157 N162 N163 L164 V167 N17 V174 V188 V2 E23 F21 V211 A215 Q216 L229

13 Page 13 Full wwpdb/emdatabank EM Map/Model Validation Report 6CV GLN TYR ALA ARG Molecule 1: Spike glycoprotein Chain C: ALA Y21 Y28 Y29 A33 F34 R35 A46 V5 I7 A1 H11 T17 T18 V19 V133 K137 Y143 K156 S157 N162 N163 L164 V167 N17 V174 V188 V2 E23 F21 V211 A215 Q216 L229 N247 N276 N283 N33 F331 L34 W341 F342 L345 I349 A35 Y351 G352 P353 V399 K43 T449 D46 A461 G462 L463 Y485 F498 V56 G57 I58 S517 N522 I526 K527 I528 R537 Y551 G56 L57 T61 R62 M63 D64 I635 N64 E646 E649 P659 L667 I677 L68 P684 V71 VAL PRO THR A711 Y712 K713 L72 K724 L738 P739 P74 Q747 I763 I769 P77 L775 R778 I784 Q822 N826 A83 T833 I85 Q856 V866 H888 V891 R895 Q9 Q99 R912 C916 G917 R92 L923 T924 I925 A929 G932 I933 V934 H937 F938 S939 Y94 T941 K957 Q963 V967 P968 R972 F975 I984 D988 R993 A994 I995 D999 I1 V11 V113 N114 K115 T119 V122 PHE PHE TRP TRP THR PRO PHE PHE TYR THR VAL PRO ARG GLN VAL GLN VAL GLN TYR ALA ARG

14 Page 14 Full wwpdb/emdatabank EM Map/Model Validation Report 6CV 4 Experimental information io Property Value Source Reconstruction method SINGLE PARTICLE Depositor Imposed symmetry POINT, C3 Depositor Number of particles used Depositor Resolution determination method FSC.143 CUT-OFF Depositor CTF correction method NONE Depositor Microscope FEI TITAN KRIOS Depositor Voltage (kv) 3 Depositor Electron dose (e /Å 2 ) Depositor Minimum defocus (nm) Not provided Depositor Maximum defocus (nm) Not provided Depositor Magnication Not provided Depositor Image detector GATAN K2 SUMMIT (4k x 4k) Depositor

15 Page 15 Full wwpdb/emdatabank EM Map/Model Validation Report 6CV 5 Model quality io 5.1 Standard geometry io Bond lengths and bond angles in the following residue types are not validated in this section: NAG 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.35 / / B.35 / / C.35 / /1639 All All.35 / /31917 There are no bond length outliers. There are no bond angle outliers. There are no chirality outliers. There are no planarity outliers. 5.2 Too-close contacts io 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 B C A B C All All The all-atom clashscore is dened as the number of clashes found per 1 atoms (including hydrogen atoms). The all-atom clashscore for this structure is 5.

16 Page 16 Full wwpdb/emdatabank EM Map/Model Validation Report 6CV All (25) 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:C:28:TYR:HD2 1:C:29:TYR:N :A:28:TYR:HD2 1:A:29:TYR:N :B:28:TYR:HD2 1:B:29:TYR:N :A:763::HG21 1:A:769::HD :B:763::HG21 1:B:769::CD :C:763::HG21 1:C:769::CD :B:763::CG2 1:B:769::HD :C:763::CG2 1:C:769::HD :C:763::HG21 1:C:769::HD :A:763::HG21 1:A:769::CD :B:763::HG21 1:B:769::HD :A:28:TYR:CD2 1:A:29:TYR:N :B:21:TYR:HB2 1:B:28:TYR:HB :B:763::CG2 1:B:769::CD :C:21:TYR:HB2 1:C:28:TYR:HB :C:28:TYR:CD2 1:C:29:TYR:N :A:21:TYR:HB2 1:A:28:TYR:HB :B:28:TYR:CD2 1:B:29:TYR:N :C:763::CG2 1:C:769::CD :A:769::HG22 2:C:125:NAG:C :A:763::CG2 1:A:769::HD :C:163::O 1:C:164::HB :A:125:NAG:C8 1:B:769::HG :A:763::CG2 1:A:769::CD :A:21:TYR:CD2 1:A:28:TYR:HB :B:125:NAG:C8 1:C:769::HG :C:21:TYR:CD2 1:C:28:TYR:HB :B:21:TYR:CD2 1:B:28:TYR:HB :C:763::HB 1:C:769::HD :A:769::HG22 2:C:125:NAG:H :B:763::HB 1:B:769::HD :B:912:ARG:HH22 1:C:9:GLN:HE :A:461:ALA:HB3 1:B:35:ARG:HH :A:35:ARG:HH22 1:C:461:ALA:HB :B:349::HG22 1:B:399:VAL:HG :C:349::HG22 1:C:399:VAL:HG :A:9:GLN:HE21 1:C:912:ARG:HH :A:912:ARG:HH22 1:B:9:GLN:HE :B:461:ALA:HB3 1:C:35:ARG:HH :C:7::O 1:C:11::NE

17 Page 17 Full wwpdb/emdatabank EM Map/Model Validation Report 6CV Atom-1 Atom-2 Interatomic Clash distance (Å) overlap (Å) 1:A:349::HG22 1:A:399:VAL:HG :A:125:NAG:H83 1:B:769::HG :A:7::O 1:A:11::NE :B:7::O 1:B:11::NE :C:283::HD21 1:C:353:PRO:HD :C:649::OE2 1:C:895:ARG:NH :B:649::OE2 1:B:895:ARG:NH :C:61:THR:HG22 1:C:932::HA :B:92:ARG:NH1 1:B:988::OD :A:283::HD21 1:A:353:PRO:HD :B:283::HD21 1:B:353:PRO:HD :B:61:THR:HG22 1:B:932::HA :B:125:NAG:H83 1:C:769::HG :A:92:ARG:NH1 1:A:988::OD :A:649::OE2 1:A:895:ARG:NH :A:61:THR:HG22 1:A:932::HA :C:92:ARG:NH1 1:C:988::OD :C:21:PHE:HB3 1:C:215:ALA:HA :B:763::CB 1:B:769::HD :C:763::CB 1:C:769::HD :B:21:PHE:HB3 1:B:215:ALA:HA :A:229::HB2 1:A:498:PHE:HZ :B:769::N 1:B:77:PRO:HD :C:769::N 1:C:77:PRO:HD :A:33:ALA:HB1 1:C:463::HD :A:21:PHE:HB3 1:A:215:ALA:HA :B:463::HD23 1:C:33:ALA:HB :B:5:VAL:HG23 1:B:2:VAL:HG :B:229::HB2 1:B:498:PHE:HZ :C:229::HB2 1:C:498:PHE:HZ :A:18:THR:HG21 2:A:1227:NAG:H :B:917::O 1:B:939::OG :C:211:VAL:H 1:C:216:GLN:HE :A:769::N 1:A:77:PRO:HD :A:917::O 1:A:939::OG :C:763::CG2 1:C:769::HD :B:21:TYR:CD2 1:B:28:TYR:CB :C:5:VAL:HG23 1:C:2:VAL:HG :A:5:VAL:HG23 1:A:2:VAL:HG :A:21:TYR:CD2 1:A:28:TYR:CB :A:463::HD23 1:B:33:ALA:HB

18 Page 18 Full wwpdb/emdatabank EM Map/Model Validation Report 6CV Atom-1 Atom-2 Interatomic Clash distance (Å) overlap (Å) 1:C:917::O 1:C:939::OG :A:211:VAL:H 1:A:216:GLN:HE :C:18:THR:HG21 2:C:1227:NAG:H :B:211:VAL:H 1:B:216:GLN:HE :B:972:ARG:NH2 1:B:999::OD :A:46::OD1 1:A:46::N :A:972:ARG:NH2 1:A:999::OD :C:21:TYR:CD2 1:C:28:TYR:CB :A:156::HB2 1:A:17::HD :B:46::N 1:B:46::OD :B:156::HB2 1:B:17::HD :C:156::HB2 1:C:17::HD :C:62:ARG:HH22 1:C:747:GLN:HB :C:972:ARG:NH2 1:C:999::OD :B:763::CG2 1:B:769::HD :C:58::HB 1:C:526::HD :B:713::NZ 1:B:724::O :C:713::NZ 1:C:724::O :A:58::HB 1:A:526::HD :A:62:ARG:HH22 1:A:747:GLN:HB :B:58::HB 1:B:526::HD :A:713::NZ 1:A:724::O :C:72::HD22 1:C:724::HD :C:276::OD1 1:C:351:TYR:OH :C:916:CYS:HB2 1:C:937::CE :B:17:THR:HG22 1:B:137::HG :B:83:ALA:HA 1:B:833:THR:HG :A:769::CG2 2:C:125:NAG:H :C:157::H 1:C:17::HB :A:916:CYS:HB2 1:A:937::CE :C:17:THR:HG22 1:C:137::HG :B:551:TYR:HE1 1:C:738::HD :C:62:ARG:HH12 1:C:747:GLN:HG :B:62:ARG:HH22 1:B:747:GLN:HB :A:157::H 1:A:17::HB :B:62:ARG:HH12 1:B:747:GLN:HG :B:916:CYS:HB2 1:B:937::CE :A:72::HD22 1:A:724::HD :A:62:ARG:HH12 1:A:747:GLN:HG :A:968:PRO:HD3 1:A:975:PHE:HE :B:667::HD13 1:B:684:PRO:HG

19 Page 19 Full wwpdb/emdatabank EM Map/Model Validation Report 6CV Atom-1 Atom-2 Interatomic Clash distance (Å) overlap (Å) 1:B:72::HD22 1:B:724::HD :C:83:ALA:HA 1:C:833:THR:HG :A:17:THR:HG22 1:A:137::HG :A:667::HD13 1:A:684:PRO:HG :A:83:ALA:HA 1:A:833:THR:HG :B:157::H 1:B:17::HB :B:85::HD11 1:B:866:VAL:HG :C:667::HD13 1:C:684:PRO:HG :C:968:PRO:HD3 1:C:975:PHE:HE :A:778:ARG:HH11 1:A:99:GLN:HB :C:46::OD1 1:C:46::N :A:85::HD11 1:A:866:VAL:HG :A:957::HB3 1:A:963:GLN:HE :A:125:NAG:H83 1:B:769::CG :A:738::HD22 1:C:551:TYR:HE :B:48:ARG:NH1 1:C:143:TYR:OH :B:778:ARG:HH11 1:B:99:GLN:HB :A:763::HB 1:A:769::HD :B:968:PRO:HD3 1:B:975:PHE:HE :C:85::HD11 1:C:866:VAL:HG :C:778:ARG:HH11 1:C:99:GLN:HB :B:957::HB3 1:B:963:GLN:HE :C:763::CB 1:C:769::CD :A:331:PHE:HE1 1:A:43::HD :B:331:PHE:HE1 1:B:43::HD :B:61:THR:HG23 1:B:62:ARG:HG :A:522::ND2 1:B:711:ALA:O :A:163::O 1:A:164::CB :A:763::CG2 1:A:769::HD :C:957::HB3 1:C:963:GLN:HE :A:247::OD1 1:A:247::N :A:61:THR:HG23 1:A:62:ARG:HG :B:113:VAL:HG12 1:B:115::H :C:63:MET:HE2 1:C:646::HG :B:164::HD12 1:B:164::HA :C:528::H 1:C:528::HG :C:61:THR:HG23 1:C:62:ARG:HG :B:163::O 1:B:164::CB :B:247::OD1 1:B:247::N :C:331:PHE:HE1 1:C:43::HD :B:276::OD1 1:B:351:TYR:OH

20 Page 2 Full wwpdb/emdatabank EM Map/Model Validation Report 6CV Atom-1 Atom-2 Interatomic Clash distance (Å) overlap (Å) 1:A:113:VAL:HG12 1:A:115::H :A:775::HD23 1:A:923::HD :C:247::OD1 1:C:247::N :B:929:ALA:HB2 1:B:934:VAL:HG :A:856:GLN:HG2 1:C:34::HD :C:929:ALA:HB2 1:C:934:VAL:HG :B:763::CB 1:B:769::CD :B:995::O 1:B:119:THR:OG :C:113:VAL:HG12 1:C:115::H :C:133:VAL:HG11 1:C:174:VAL:HB :A:33::ND2 1:B:856:GLN:OE :B:46:ALA:HA 1:B:23::HA :C:19:VAL:HG11 1:C:167:VAL:HG :A:133:VAL:HG11 1:A:174:VAL:HB :A:63:MET:HE2 1:A:646::HG :B:63:MET:HE2 1:B:646::HG :B:133:VAL:HG11 1:B:174:VAL:HB :A:711:ALA:O 1:C:522::ND :C:56:VAL:HG13 1:C:56::HA :A:929:ALA:HB2 1:A:934:VAL:HG :B:57::HD12 1:B:941:THR:HG :B:775::HD23 1:B:923::HD :C:995::O 1:C:119:THR:OG :A:517::O 1:A:537:ARG:NH :B:739:PRO:HA 1:B:74:PRO:HD :A:19:VAL:HG11 1:A:167:VAL:HG :C:517::O 1:C:537:ARG:NH :B:517::O 1:B:537:ARG:NH :A:46:ALA:HA 1:A:23::HA :A:995::O 1:A:119:THR:OG :A:551:TYR:HE1 1:B:738::HD :B:528::HG13 1:B:528::H :C:775::HD23 1:C:923::HD :B:522::ND2 1:C:711:ALA:O :C:64::N 1:C:64::OD :B:19:VAL:HG11 1:B:167:VAL:HG :B:56:VAL:HG13 1:B:56::HA :A:57::HD12 1:A:941:THR:HG :C:46:ALA:HA 1:C:23::HA :C:57::HD12 1:C:941:THR:HG :A:56:VAL:HG13 1:A:56::HA

21 Page 21 Full wwpdb/emdatabank EM Map/Model Validation Report 6CV Atom-1 Atom-2 Interatomic Clash distance (Å) overlap (Å) 1:A:68::HD21 1:A:925::HG :B:658::HA 1:B:659:PRO:HD :C:449:THR:HB 1:C:485:TYR:H :C:68::HD21 1:C:925::HG :A:342:PHE:HD2 1:A:345::HD :B:967:VAL:HB 1:B:11:VAL:HB :A:48:ARG:NH1 1:B:143:TYR:OH :A:449:THR:HB 1:A:485:TYR:H :B:449:THR:HB 1:B:485:TYR:H :C:635::HD12 1:C:635::HA :A:163::O 1:A:164::HB :C:163::O 1:C:164::CB :A:856:GLN:OE1 1:C:33::ND :C:967:VAL:HB 1:C:11:VAL:HB :C:342:PHE:HD2 1:C:345::HD :C:822:GLN:NE2 1:C:826::OD :A:1:ALA:HB2 1:A:188:VAL:HG :A:276::OD1 1:A:351:TYR:OH :A:89:ARG:HH12 1:A:894:GLN:HE :B:116::HD2 1:B:123:THR:HA :B:975:PHE:HB3 1:B:984::HG :C:975:PHE:HB3 1:C:984::HG :C:677::HG13 1:C:677::H :C:739:PRO:HA 1:C:74:PRO:HD :A:632:CYS:HA 1:A:635::HG :A:658::HA 1:A:659:PRO:HD :B:1:ALA:HB2 1:B:188:VAL:HG :C:1:ALA:HA 1:C:188:VAL:HA :A:458::HD23 1:A:458::HA :A:975:PHE:HB3 1:A:984::HG :B:163::O 1:B:164::HB :B:342:PHE:HD2 1:B:345::HD :B:68::HD21 1:B:925::HG :B:33::ND2 1:C:856:GLN:OE :B:11:VAL:HG22 1:C:993:ARG:HH :A:116::HD2 1:A:123:THR:HA :A:261::HB3 1:A:265:THR:HG :B:1:ALA:HA 1:B:188:VAL:HA :B:122:NAG:H61 2:B:1221:NAG:N :B:632:CYS:HA 1:B:635::HG :A:635::HD12 1:A:635::HA

22 Page 22 Full wwpdb/emdatabank EM Map/Model Validation Report 6CV Atom-1 Atom-2 Interatomic Clash distance (Å) overlap (Å) 1:B:491:CYS:SG 1:B:492::N :C:1:ALA:HB2 1:C:188:VAL:HG :C:888::HA 1:C:891:VAL:HG :A:34::HD11 1:B:856:GLN:HG :A:967:VAL:HB 1:A:11:VAL:HB There are no symmetry-related clashes. 5.3 Torsion angles io Protein backbone io 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. Mol Chain Analysed Favoured Allowed Outliers Percentiles 1 A 989/115 (9%) 857 (87%) 13 (13%) 2 (%) B 989/115 (9%) 854 (86%) 133 (13%) 2 (%) C 989/115 (9%) 855 (86%) 132 (13%) 2 (%) All All 2967/3315 (9%) 2566 (86%) 395 (13%) 6 (%) All (6) Ramachandran outliers are listed below: Mol Chain Res Type 1 A 17 1 B 17 1 C 17 1 A 659 PRO 1 B 659 PRO 1 C 659 PRO Protein sidechains io 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

23 Page 23 Full wwpdb/emdatabank EM Map/Model Validation Report 6CV 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 849/953 (89%) 845 (1%) 4 (%) B 849/953 (89%) 845 (1%) 4 (%) C 849/953 (89%) 845 (1%) 4 (%) 9 95 All All 2547/2859 (89%) 2535 (1%) 12 (%) 9 95 All (12) residues with a non-rotameric sidechain are listed below: Mol Chain Res Type 1 A 28 TYR 1 A A 64 1 A B 28 TYR 1 B B 64 1 B C 28 TYR 1 C C 64 1 C 784 Some sidechains can be ipped to improve hydrogen bonding and reduce clashes. All (28) such sidechains are listed below: Mol Chain Res Type 1 A 41 1 A 43 1 A A 216 GLN 1 A 41 GLN 1 A A 894 GLN 1 A 9 GLN 1 A 963 GLN 1 B 41 1 B 43 1 B B 216 GLN

24 Page 24 Full wwpdb/emdatabank EM Map/Model Validation Report 6CV Mol Chain Res Type 1 B 41 GLN 1 B B 894 GLN 1 B 9 GLN 1 B 963 GLN 1 C 41 1 C 43 1 C C 17 1 C 216 GLN 1 C 41 GLN 1 C C 894 GLN 1 C 9 GLN 1 C 963 GLN RNA io There are no RNA molecules in this entry. 5.4 Non-standard residues in protein, DNA, RNA chains io There are no non-standard protein/dna/rna residues in this entry. 5.5 Carbohydrates io There are no carbohydrates in this entry. 5.6 Ligand geometry io 87 ligands are modelled in this entry. In the following table, the Counts columns list the number of bonds (or angles) for which Mogul statistics could be retrieved, the number of bonds (or angles) that are observed in the model and the number of bonds (or angles) that are dened in the Chemical Component Dictionary. The Link column lists molecule types, if any, to which the group is linked. 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 > 2 is considered an outlier worth inspection. RMSZ is the root-mean-square of all Z scores of the bond lengths (or angles).

25 Page 25 Full wwpdb/emdatabank EM Map/Model Validation Report 6CV Mol Type Chain Res Link Bond lengths Bond angles Counts RMSZ # Z > 2 Counts RMSZ # Z > 2 2 NAG A ,14, ,19, NAG A ,14, ,19, NAG A ,14, ,19, NAG A ,14, ,19, NAG A 125 1,2 14,14, ,19, NAG A ,14, ,19, NAG A ,14, ,19, NAG A 128 1,2 14,14, ,19, NAG A ,14, ,19, NAG A 121 1,2 14,14, ,19, NAG A ,14, ,19, NAG A ,14, ,19, NAG A ,14, ,19, (5%) 2 NAG A ,2 14,14, ,19, NAG A ,14, ,19, (5%) 2 NAG A ,14, ,19, NAG A ,14, ,19, (5%) 2 NAG A ,14, ,19, NAG A ,14, ,19, NAG A 122 1,2 14,14, ,19, (5%) 2 NAG A ,14, ,19, NAG A ,14, ,19, (5%) 2 NAG A ,2 14,14, ,19, NAG A ,14, ,19, NAG A ,14, ,19, NAG A ,14, ,19, NAG A ,2 14,14, ,19, NAG A ,14, ,19, NAG A ,14, ,19, NAG B ,14, ,19, NAG B ,14, ,19, NAG B ,14, ,19, NAG B ,14, ,19, NAG B 125 1,2 14,14, ,19, NAG B ,14, ,19, NAG B ,14, ,19, NAG B 128 1,2 14,14, ,19, NAG B ,14, ,19, NAG B 121 1,2 14,14, ,19, NAG B ,14, ,19, NAG B ,14, ,19, NAG B ,14, ,19,21.51

26 Page 26 Full wwpdb/emdatabank EM Map/Model Validation Report 6CV Mol Type Chain Res Link Bond lengths Bond angles Counts RMSZ # Z > 2 Counts RMSZ # Z > 2 2 NAG B ,2 14,14, ,19, NAG B ,14, ,19, NAG B ,14, ,19, NAG B ,14, ,19, (5%) 2 NAG B ,14, ,19, NAG B ,14, ,19, NAG B 122 1,2 14,14, ,19, (5%) 2 NAG B ,14, ,19, NAG B ,14, ,19, (5%) 2 NAG B ,2 14,14, ,19, NAG B ,14, ,19, NAG B ,14, ,19, NAG B ,14, ,19, NAG B ,2 14,14, ,19, NAG B ,14, ,19, NAG B ,14, ,19, NAG C ,14, ,19, NAG C ,14, ,19, NAG C ,14, ,19, NAG C ,14, ,19, NAG C 125 1,2 14,14, ,19, NAG C ,14, ,19, NAG C ,14, ,19, NAG C 128 1,2 14,14, ,19, NAG C ,14, ,19, (5%) 2 NAG C 121 1,2 14,14, ,19, NAG C ,14, ,19, NAG C ,14, ,19, NAG C ,14, ,19, NAG C ,2 14,14, ,19, NAG C ,14, ,19, NAG C ,14, ,19, NAG C ,14, ,19, (5%) 2 NAG C ,14, ,19, NAG C ,14, ,19, NAG C 122 1,2 14,14, ,19, (5%) 2 NAG C ,14, ,19, NAG C ,14, ,19, (5%) 2 NAG C ,2 14,14, ,19, NAG C ,14, ,19, NAG C ,14, ,19,21.63

27 Page 27 Full wwpdb/emdatabank EM Map/Model Validation Report 6CV Mol Type Chain Res Link Bond lengths Bond angles Counts RMSZ # Z > 2 Counts RMSZ # Z > 2 2 NAG C ,14, ,19, NAG C ,2 14,14, ,19, NAG C ,14, ,19, NAG C ,14, ,19,21.58 In the following table, the Chirals column lists the number of chiral outliers, the number of chiral centers analysed, the number of these observed in the model and the number dened in the Chemical Component Dictionary. Similar counts are reported in the Torsion and Rings columns. '-' means no outliers of that kind were identied. Mol Type Chain Res Link Chirals Torsions Rings 2 NAG A /6/23/26 /1/1/1 2 NAG A /6/23/26 /1/1/1 2 NAG A /6/23/26 /1/1/1 2 NAG A /6/23/26 /1/1/1 2 NAG A 125 1,2 - /6/23/26 /1/1/1 2 NAG A /6/23/26 /1/1/1 2 NAG A /6/23/26 /1/1/1 2 NAG A 128 1,2 - /6/23/26 /1/1/1 2 NAG A /6/23/26 /1/1/1 2 NAG A 121 1,2 - /6/23/26 /1/1/1 2 NAG A /6/23/26 /1/1/1 2 NAG A /6/23/26 /1/1/1 2 NAG A /6/23/26 /1/1/1 2 NAG A ,2 - /6/23/26 /1/1/1 2 NAG A /6/23/26 /1/1/1 2 NAG A /6/23/26 /1/1/1 2 NAG A /6/23/26 /1/1/1 2 NAG A /6/23/26 /1/1/1 2 NAG A /6/23/26 /1/1/1 2 NAG A 122 1,2 - /6/23/26 /1/1/1 2 NAG A /6/23/26 /1/1/1 2 NAG A /6/23/26 /1/1/1 2 NAG A ,2 - /6/23/26 /1/1/1 2 NAG A /6/23/26 /1/1/1 2 NAG A /6/23/26 /1/1/1 2 NAG A /6/23/26 /1/1/1 2 NAG A ,2 - /6/23/26 /1/1/1 2 NAG A /6/23/26 /1/1/1 2 NAG A /6/23/26 /1/1/1 2 NAG B /6/23/26 /1/1/1 2 NAG B /6/23/26 /1/1/1 2 NAG B /6/23/26 /1/1/1

28 Page 28 Full wwpdb/emdatabank EM Map/Model Validation Report 6CV Mol Type Chain Res Link Chirals Torsions Rings 2 NAG B /6/23/26 /1/1/1 2 NAG B 125 1,2 - /6/23/26 /1/1/1 2 NAG B /6/23/26 /1/1/1 2 NAG B /6/23/26 /1/1/1 2 NAG B 128 1,2 - /6/23/26 /1/1/1 2 NAG B /6/23/26 /1/1/1 2 NAG B 121 1,2 - /6/23/26 /1/1/1 2 NAG B /6/23/26 /1/1/1 2 NAG B /6/23/26 /1/1/1 2 NAG B /6/23/26 /1/1/1 2 NAG B ,2 - /6/23/26 /1/1/1 2 NAG B /6/23/26 /1/1/1 2 NAG B /6/23/26 /1/1/1 2 NAG B /6/23/26 /1/1/1 2 NAG B /6/23/26 /1/1/1 2 NAG B /6/23/26 /1/1/1 2 NAG B 122 1,2 - /6/23/26 /1/1/1 2 NAG B /6/23/26 /1/1/1 2 NAG B /6/23/26 /1/1/1 2 NAG B ,2 - /6/23/26 /1/1/1 2 NAG B /6/23/26 /1/1/1 2 NAG B /6/23/26 /1/1/1 2 NAG B /6/23/26 /1/1/1 2 NAG B ,2 - /6/23/26 /1/1/1 2 NAG B /6/23/26 /1/1/1 2 NAG B /6/23/26 /1/1/1 2 NAG C /6/23/26 /1/1/1 2 NAG C /6/23/26 /1/1/1 2 NAG C /6/23/26 /1/1/1 2 NAG C /6/23/26 /1/1/1 2 NAG C 125 1,2 - /6/23/26 /1/1/1 2 NAG C /6/23/26 /1/1/1 2 NAG C /6/23/26 /1/1/1 2 NAG C 128 1,2 - /6/23/26 /1/1/1 2 NAG C /6/23/26 /1/1/1 2 NAG C 121 1,2 - /6/23/26 /1/1/1 2 NAG C /6/23/26 /1/1/1 2 NAG C /6/23/26 /1/1/1 2 NAG C /6/23/26 /1/1/1 2 NAG C ,2 - /6/23/26 /1/1/1 2 NAG C /6/23/26 /1/1/1 2 NAG C /6/23/26 /1/1/1

29 Page 29 Full wwpdb/emdatabank EM Map/Model Validation Report 6CV Mol Type Chain Res Link Chirals Torsions Rings 2 NAG C /6/23/26 /1/1/1 2 NAG C /6/23/26 /1/1/1 2 NAG C /6/23/26 /1/1/1 2 NAG C 122 1,2 - /6/23/26 /1/1/1 2 NAG C /6/23/26 /1/1/1 2 NAG C /6/23/26 /1/1/1 2 NAG C ,2 - /6/23/26 /1/1/1 2 NAG C /6/23/26 /1/1/1 2 NAG C /6/23/26 /1/1/1 2 NAG C /6/23/26 /1/1/1 2 NAG C ,2 - /6/23/26 /1/1/1 2 NAG C /6/23/26 /1/1/1 2 NAG C /6/23/26 /1/1/1 There are no bond length outliers. All (12) bond angle outliers are listed below: Mol Chain Res Type Atoms Z Observed( o ) Ideal( o ) 29 NAG C1-O5-C NAG C1-O5-C NAG C1-O5-C NAG C1-O5-C NAG C1-O5-C NAG C1-O5-C NAG C1-O5-C NAG C1-O5-C NAG C1-O5-C NAG C1-O5-C NAG C1-O5-C NAG C1-O5-C There are no chirality outliers. There are no torsion outliers. There are no ring outliers. 7 monomers are involved in 11 short contacts: Mol Chain Res Type Clashes Symm-Clashes 25 NAG NAG 1 25 NAG 2

30 Page 3 Full wwpdb/emdatabank EM Map/Model Validation Report 6CV Mol Chain Res Type Clashes Symm-Clashes 22 NAG NAG 1 25 NAG NAG Other polymers io There are no such residues in this entry. 5.8 Polymer linkage issues io There are no chain breaks in this entry.