Full wwpdb X-ray Structure Validation Report i Mar 8, 2018 04:49 pm GMT PDB ID : 3GHG Title : Crystal Structure of Human Fibrinogen Authors : Doolittle, R.F.; Kollman, J.M.; Sawaya, M.R.; Pandi, L.; Riley, M. Deposited on : 2009-03-03 Resolution : 2.90 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 https://www.wwpdb.org/validation/2017/xrayvalidationreporthelp 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 Mogul : 1.7.3 (157068), CSD as539be (2018) Xtriage (Phenix) : 1.13 EDS : trunk30967 Percentile statistics : 20171227.v01 (using entries in the PDB archive December 27th 2017) Refmac : 5.8.0158 CCP4 : 7.0 (Gargrove) Ideal geometry (proteins) : Engh & Huber (2001) Ideal geometry (DNA, RNA) : Parkinson et al. (1996) Validation Pipeline (wwpdb-vp) : trunk30967
Page 2 Full wwpdb X-ray Structure Validation Report 3GHG 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 2.90 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 111664 1716 (2.90-2.90) Clashscore 122126 1924 (2.90-2.90) Ramachandran outliers 120053 1884 (2.90-2.90) Sidechain outliers 120020 1886 (2.90-2.90) RSRZ outliers 108989 1669 (2.90-2.90) 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 A 562 1 D 562 1 G 562 1 J 562 2 B 461 2 E 461
Page 3 Full wwpdb X-ray Structure Validation Report 3GHG Mol Chain Length Quality of chain 2 H 461 2 K 461 3 C 411 3 F 411 3 I 411 3 L 411 4 M 4 4 N 4 4 Q 4 4 R 4 5 O 4 5 P 4 5 S 4 5 T 4 The following table lists non-polymeric compounds, carbohydrate monomers and non-standard residues in protein, DNA, RNA chains that are outliers for geometric or electron-density-fit criteria: Mol Type Chain Res Chirality Geometry Clashes Electron density 10 GAL B 476 - - - X 10 GAL B 478 X - - - 10 GAL E 476 - - - X 10 GAL E 478 X - - X 10 GAL K 476 - - - X 10 GAL K 478 X - - X 11 SIA B 479 - - - X 11 SIA B 480 - - - X 11 SIA E 480 - - - X 11 SIA K 479 - - - X 11 SIA K 480 - - - X 6 NAG B 470 - - X - 6 NAG E 470 X - - -
Page 4 Full wwpdb X-ray Structure Validation Report 3GHG Mol Type Chain Res Chirality Geometry Clashes Electron density 6 NAG H 470 X - - - 6 NAG K 470 - - X - 6 NAG L 570 - - X X 6 NAG L 571 - - - X 7 NDG B 475 - - - X 7 NDG B 477 - - - X 7 NDG E 475 - - - X 7 NDG E 477 - - - X 7 NDG K 471 - - - X 7 NDG K 475 - - - X 7 NDG K 477 - - - X 8 BMA K 472 - - - X 9 MAN B 473 - - - X 9 MAN B 474 - - - X 9 MAN E 473 - - - X 9 MAN E 474 - - - X 9 MAN H 473 - - - X 9 MAN H 474 - - - X 9 MAN K 474 - - - X
Page 5 Full wwpdb X-ray Structure Validation Report 3GHG 2 Entry composition i There are 12 unique types of molecules in this entry. The entry contains 31833 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 protein called Fibrinogen alpha chain. Mol Chain Residues Atoms ZeroOcc AltConf Trace 1 A 174 Total C N O S 1431 876 268 278 9 0 0 0 1 D 174 Total C N O S 1431 876 268 278 9 0 0 0 1 G 174 Total C N O S 1431 876 268 278 9 0 0 0 1 J 186 Total C N O S 1527 941 284 292 10 0 0 0 Molecule 2 is a protein called Fibrinogen beta chain. Mol Chain Residues Atoms ZeroOcc AltConf Trace 2 B 401 Total C N O S 3209 1995 564 624 26 0 0 0 2 E 401 Total C N O S 3209 1995 564 624 26 0 0 0 2 H 401 Total C N O S 3209 1995 564 624 26 0 0 0 2 K 401 Total C N O S 3209 1995 564 624 26 0 0 0 Molecule 3 is a protein called Fibrinogen gamma chain. Mol Chain Residues Atoms ZeroOcc AltConf Trace 3 C 381 Total C N O S 3050 1931 510 593 16 0 0 0 3 F 382 Total C N O S 3054 1933 511 594 16 0 0 0 3 I 394 Total C N O S 3145 1986 527 614 18 0 0 0 3 L 391 Total C N O S 3126 1974 524 610 18 0 0 0
Page 6 Full wwpdb X-ray Structure Validation Report 3GHG There are 12 discrepancies between the modelled and reference sequences: Chain Residue Modelled Actual Comment Reference C 408 - SEE REMARK 999 UNP P02679 C 409 - SEE REMARK 999 UNP P02679 C 410 - SEE REMARK 999 UNP P02679 F 408 - SEE REMARK 999 UNP P02679 F 409 - SEE REMARK 999 UNP P02679 F 410 - SEE REMARK 999 UNP P02679 I 408 - SEE REMARK 999 UNP P02679 I 409 - SEE REMARK 999 UNP P02679 I 410 - SEE REMARK 999 UNP P02679 L 408 - SEE REMARK 999 UNP P02679 L 409 - SEE REMARK 999 UNP P02679 L 410 - SEE REMARK 999 UNP P02679 Molecule 4 is a protein called A knob. Mol Chain Residues Atoms ZeroOcc AltConf Trace 4 M 4 Total C N O 30 18 7 5 0 0 0 4 N 4 Total C N O 30 18 7 5 0 0 0 4 Q 4 Total C N O 30 18 7 5 0 0 0 4 R 4 Total C N O 30 18 7 5 0 0 0 Molecule 5 is a protein called B knob. Mol Chain Residues Atoms ZeroOcc AltConf Trace 5 O 4 Total C N O 33 19 9 5 0 0 0 5 P 4 Total C N O 33 19 9 5 0 0 0 5 S 4 Total C N O 33 19 9 5 0 0 0 5 T 4 Total C N O 33 19 9 5 0 0 0 Molecule 6 is N-ACETYL-D-COSAMINE (three-letter code: NAG) (formula: C 8 H 15 NO 6 ).
Page 7 Full wwpdb X-ray Structure Validation Report 3GHG Mol Chain Residues Atoms ZeroOcc AltConf 6 B 1 Total C N O 14 8 1 5 0 0 6 E 1 Total C N O 14 8 1 5 0 0 6 H 1 Total C N O 14 8 1 5 0 0 6 K 1 Total C N O 14 8 1 5 0 0 6 L 1 Total C N O 14 8 1 5 0 0 6 L 1 Total C N O 14 8 1 5 0 0 Molecule 7 is 2-(ACETYLAMINO)-2-DEOXY-A-D-COPYRANOSE (three-letter code: NDG) (formula: C 8 H 15 NO 6 ).
Page 8 Full wwpdb X-ray Structure Validation Report 3GHG Mol Chain Residues Atoms ZeroOcc AltConf 7 B 1 Total C N O 14 8 1 5 0 0 7 B 1 Total C N O 14 8 1 5 0 0 7 B 1 Total C N O 14 8 1 5 0 0 7 E 1 Total C N O 14 8 1 5 0 0 7 E 1 Total C N O 14 8 1 5 0 0 7 E 1 Total C N O 14 8 1 5 0 0 7 H 1 Total C N O 14 8 1 5 0 0 7 K 1 Total C N O 14 8 1 5 0 0 7 K 1 Total C N O 14 8 1 5 0 0 7 K 1 Total C N O 14 8 1 5 0 0 Molecule 8 is BETA-D-MANNOSE (three-letter code: BMA) (formula: C 6 H 12 O 6 ).
Page 9 Full wwpdb X-ray Structure Validation Report 3GHG Mol Chain Residues Atoms ZeroOcc AltConf 8 B 1 Total C O 11 6 5 0 0 8 E 1 Total C O 11 6 5 0 0 8 H 1 Total C O 11 6 5 0 0 8 K 1 Total C O 11 6 5 0 0 Molecule 9 is ALPHA-D-MANNOSE (three-letter code: MAN) (formula: C 6 H 12 O 6 ).
Page 10 Full wwpdb X-ray Structure Validation Report 3GHG Mol Chain Residues Atoms ZeroOcc AltConf 9 B 1 Total C O 11 6 5 0 0 9 B 1 Total C O 11 6 5 0 0 9 E 1 Total C O 11 6 5 0 0 9 E 1 Total C O 11 6 5 0 0 9 H 1 Total C O 11 6 5 0 0 9 H 1 Total C O 11 6 5 0 0 9 K 1 Total C O 11 6 5 0 0 9 K 1 Total C O 11 6 5 0 0 Molecule 10 is BETA-D-GCTOSE (three-letter code: GAL) (formula: C 6 H 12 O 6 ). Mol Chain Residues Atoms ZeroOcc AltConf 10 B 1 Total C O 11 6 5 0 0 10 B 1 Total C O 11 6 5 0 0 10 E 1 Total C O 11 6 5 0 0 10 E 1 Total C O 11 6 5 0 0
Page 11 Full wwpdb X-ray Structure Validation Report 3GHG Mol Chain Residues Atoms ZeroOcc AltConf 10 K 1 Total C O 11 6 5 0 0 10 K 1 Total C O 11 6 5 0 0 Molecule 11 is O-SIALIC ACID (three-letter code: SIA) (formula: C 11 H 19 NO 9 ). Mol Chain Residues Atoms ZeroOcc AltConf 11 B 1 Total C N O 20 11 1 8 0 0 11 B 1 Total C N O 20 11 1 8 0 0 11 E 1 Total C N O 20 11 1 8 0 0 11 E 1 Total C N O 20 11 1 8 0 0 11 K 1 Total C N O 20 11 1 8 0 0 11 K 1 Total C N O 20 11 1 8 0 0 Molecule 12 is CALCIUM ION (three-letter code: CA) (formula: Ca). Mol Chain Residues Atoms ZeroOcc AltConf Total Ca 12 K 1 0 0 1 1
Page 12 Full wwpdb X-ray Structure Validation Report 3GHG Mol Chain Residues Atoms ZeroOcc AltConf Total Ca 12 E 1 0 0 1 1 Total Ca 12 H 1 0 0 1 1 Total Ca 12 B 1 0 0 1 1 Total Ca 12 I 1 0 0 1 1 Total Ca 12 C 1 0 0 1 1 Total Ca 12 L 1 0 0 1 1 Total Ca 12 F 1 0 0 1 1
Page 13 Full wwpdb X-ray Structure Validation Report 3GHG 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: Fibrinogen alpha chain Chain A: ILE ILE TYR CYS MET ILE MET TYR CYS ILE TRP TRP TRP TRP TRP TRP TRP MET MET MET ILE TYR TRP E151 V152 I156 S160 C161 R162 C165 L169 A170 R171 L175 K176 Q181 Q184 L185 V188 I189 D192 L193 L194 P195 S196 R197 Q200 ILE MET N79 N80 K81 D82 S83 H84 S85 L86 N89 I90 M91 E92 I93 L94 R95 G96 S99 N102 N103 R104 D105 N106 T107 Y108 N109 R110 V111 S112 L115 I119 L122 K123 V126 K129 I133 Q134 L135 L136 Q137 K138 N139 V140 R141 A142 Q143 L144 M147 K148 R149 L150 A27 C28 K29 D30 E39 D40 W41 N42 P46 S47 G48 K52 I55 V58 N59 T63 N64 R65 I66 L69 K70 N71 S72 L73 Y76 Molecule 1: Fibrinogen alpha chain Chain D: A27 C28 K29 D30 S31 D32 W33 P34 S37 W41 N42 Y43 K44 C45 P46 S47 G48 C49 R50 M51 K52 I55 N59 T63 N64 R65 I66 N67 K68
Page 14 Full wwpdb X-ray Structure Validation Report 3GHG L69 L73 F74 E75 Y76 N79 N80 K81 D82 S83 H84 S85 L86 T87 T88 N89 I90 M91 E92 I93 L94 R95 G96 D97 F98 S99 S100 A101 N102 N103 N106 T107 Y108 N109 R110 V111 S112 E113 D114 L115 R116 S117 R118 I119 L122 K123 I127 Q131 Q134 L135 L136 Q137 K138 N139 V140 R141 A142 Q143 L144 R149 L150 E151 V152 D153 I156 S160 C161 R162 A168 L169 A170 R171 E172 V173 D174 Q181 Q182 L185 E186 I189 A190 K191 D192 L193 L194 P195 S196 Q200 ILE MET TRP MET MET MET ILE TYR TRP TRP TRP TRP TRP TRP TRP TYR CYS ILE CYS MET ILE MET ILE ILE TYR Molecule 1: Fibrinogen alpha chain Chain G: A27 C28 K29 D30 S31 D32 W33 P34 W41 N42 C45 P46 S47 G48 K52 I55 V58 N59 Q60 D61 F62 T63 N64 R65 I66 N67 K68 L69 K70 N71 S72 L73 F74 E75 N79 I93 L94 R95 G96 D97 F98 S99 S100 A101 R104 D105 Y108 L115 R116 S117 R118 I119 L122 K123 V126 I133 Q134 L135 L136 Q137 K138 N139 A142 Q143 L144 V145 D146 M147 L150 I154 D155 I156 K157 S160 C165 S166 L169 A170 Q182 K183 Q184 L185 V188 I189 P195 Q200 ILE MET TRP MET MET MET ILE TYR TRP TRP TRP TRP TRP TRP TRP TYR CYS ILE CYS MET ILE MET ILE
Page 15 Full wwpdb X-ray Structure Validation Report 3GHG ILE TYR Molecule 1: Fibrinogen alpha chain Chain J: A27 C28 K29 P34 F35 D38 E39 D40 W41 N42 Y43 K44 C45 P46 M51 L54 I55 V58 N59 Q60 D61 F62 T63 N64 R65 I66 N67 K68 L69 K70 N71 S72 L73 F74 E75 Y76 Q77 N80 K81 D82 S83 H84 I93 L94 N106 T107 Y108 N109 R110 V111 S112 E113 D114 L115 R116 S117 R118 I119 E120 V121 L122 K123 V126 I127 E128 K129 V130 Q131 H132 I133 L136 Q137 K138 N139 V140 R141 L144 V145 D146 M147 K148 R149 L150 E151 V152 D153 I154 D155 I156 R159 R162 R167 A168 L169 A170 R171 E172 V173 D174 L175 Y178 Q181 Q182 K183 Q184 L194 P195 S196 R197 D198 R199 Q200 H201 L202 P203 L204 I205 K206 M207 K208 P209 V210 P211 D212 TRP MET MET MET ILE TYR TRP TRP TRP TRP TRP TRP TRP TYR CYS ILE CYS MET ILE MET ILE ILE TYR Molecule 2: Fibrinogen beta chain Chain B: ILE TYR K58 A59 P60 L66 H67 A68 D69 L75 T78 G79 C80 Q81 L82 Q83 E84 A85 L86 L87 Q88 Q89 E90 R91 P92 I93 R94 V97 D98 E99 L100 N101 N102 N103 V104 E105 A106 V107 S108 Q109 S112 S113 S114 F115 Q116 Y117 M118 Y119 D123 L124 W125 Q126 K127 R128 Q129 D134 N135 E136 N137 V138 V139 N140 E141 Y142 S143 S144 E145 L146 H149 Q150 L151 Y152 I153 D154 E155 T156 V157 N158 S159 N160 I161 P162 T163 N164 L165 R166 V167 L168 R169 S170 I171 L172 L175 R176 S177 K178 I179 Q180 K181 L182 E183 S184 D185 V186 S187 A188 Q189 P196 C197 T198 V199 S200 C201 N202 I203 P204 V205 K209 E210 C211 E212 E213 I214 I215 E223 M224 Y225 L226 I227 D230 V233 K234 R237 V238 Y239 C240 D241 W249 T250 V251 I252 Q253 N254 R255 Q256 D257 G258 S259 V260 R264 K265 W266 D267 P268 Y269 K270 F273 V276 T280 D281 G282 K283 N284 G287
Page 16 Full wwpdb X-ray Structure Validation Report 3GHG D381 W385 L386 T387 Q393 G399 W403 Y404 N405 R406 C407 H408 A409 R415 G420 M426 D432 D433 G434 V435 V436 W437 M438 K441 Y445 S451 I454 F457 F458 E291 Y292 W293 L294 G295 N296 D297 K298 I299 S300 T303 L311 I312 E313 W317 K318 G319 D320 K321 H325 F329 T330 V331 I340 S341 V342 N343 K344 Y345 R346 N351 A352 L353 M354 Q359 L360 N364 M367 T368 I369 H370 N371 G372 M373 S376 T377 R380 Molecule 2: Fibrinogen beta chain Chain E: I454 F458 H370 N371 G372 M373 S376 R380 D381 N382 W385 L386 T387 C394 E397 W402 W403 Y404 N405 R406 C407 H408 A409 A410 N411 P412 R415 Q421 Y422 T423 W424 D425 M426 A427 T431 D432 D433 G434 V435 V436 W437 M438 N439 S443 W444 M447 R448 K449 M452 K453 G295 N296 D297 K298 I299 S300 Q301 L302 T303 T308 E309 L310 L311 I312 E313 M314 E315 D316 D320 K321 V322 K323 A324 H325 Y326 T330 V331 Q332 N333 E334 A335 Q339 I340 S341 V342 N343 K344 Y345 R346 G347 T348 N351 A352 L353 M354 D355 G356 Q359 L360 E363 T368 I369 I215 R216 K217 G218 G219 S222 L226 I227 Q228 S231 S232 V233 K234 P235 Y236 R237 V238 Y239 C240 D241 M242 N243 T244 V251 I252 Q253 Q256 D257 G258 S259 V260 G263 R264 K265 W266 D267 P268 Y269 K270 N275 N279 T280 D281 N284 P289 G290 E291 Y292 W293 L294 E145 L146 E147 K148 H149 Q150 L151 Y152 I153 D154 E155 T156 V157 N158 S159 N160 I161 P162 T163 N164 L165 R166 V167 L168 R169 S170 I171 L172 R176 S177 K178 I179 Q180 K181 L182 D185 V186 S187 A188 Q189 M190 E191 T198 V199 S200 I203 P204 V205 V206 K209 E210 C211 E212 E213 I214 A62 G63 G64 D69 P70 D71 L72 G73 V74 P77 L82 L86 E90 R91 P92 I93 L100 V104 E105 A106 V107 S108 S111 S112 S113 S114 F115 Q116 Y117 M118 Y119 L120 L121 K122 D123 L124 W125 Q126 K130 Q131 N135 E136 N137 V138 V139 N140 E141 Y142 S143 S144 ILE TYR K58 A59 Molecule 2: Fibrinogen beta chain Chain H: K234 P235 Y236 R237 V238 T250 V251 I252 Q253 Q256 D257 G258 S259 V260 D261 D267 P268 Y269 K270 Q271 N279 T280 N284 E291 G295 N296 I299 S300 Q301 L302 T308 E309 L310 L311 I312 E313 M314 E315 D316 D320 K321 V322 K323 Y326 F329 T330 V331 Q332 E141 Y142 E147 K148 H149 Y152 I153 V157 N164 V167 L168 I171 L172 E173 N174 L175 R176 S177 K178 I179 Q180 K181 L182 E183 S184 D185 E191 T195 P196 S200 C201 N202 I203 P204 V205 V206 K209 E210 C211 E212 E213 G219 M224 Y225 L226 S232 V233 D61 L66 H67 A68 L72 G73 V74 L75 T78 Q81 L82 Q83 L87 R91 P92 E99 L100 N101 N102 N103 V104 E105 A106 V107 S108 Q109 T110 S111 S112 S113 S114 F115 Q116 Y117 M118 Y119 L120 L121 K122 D123 L124 W125 Q126 K127 R128 V132 N135 V138 V139 N140 ILE TYR K58 A59 P60
Page 17 Full wwpdb X-ray Structure Validation Report 3GHG N333 E334 A335 N336 K337 Y338 V342 N343 A349 G350 N351 A352 L353 M354 Q359 L360 M361 G362 E363 N364 M367 M373 F374 R380 W385 L386 T387 C394 E397 D398 W402 W403 Y404 N405 R406 C407 A410 N413 G414 R415 Y416 Y417 G420 Q421 Y422 T431 D432 D433 G434 V435 V436 W437 M438 N439 W444 Y445 S446 M450 S451 M452 K453 I454 F458 Molecule 2: Fibrinogen beta chain Chain K: ILE TYR K58 A59 P60 L66 T78 Q83 E84 A85 L86 R91 P92 I93 R94 N95 S96 L100 N101 N102 N103 V104 E105 A106 V107 S112 F115 M118 Y119 L120 L121 K122 W125 R128 Q129 K130 Q131 V132 K133 D134 N135 E136 N137 V138 V139 N140 E141 S144 E145 L146 E147 K148 H149 Q150 L151 Y152 I153 D154 V157 N158 P162 V167 L168 R169 S170 I171 L172 E173 N174 I179 E183 S184 D185 V186 S187 A188 Q189 Y192 V199 S200 C201 V205 K209 E210 C211 E212 I215 G219 M224 Y225 L226 I227 Q228 P229 D230 V233 R237 V238 D241 M242 W249 I252 Q253 N254 R255 Q256 D257 G258 S259 W266 D267 P268 G272 N275 V276 T280 D281 E291 Y292 W293 L294 G295 N296 D297 K298 I299 S300 Q301 L302 L310 L311 I312 E313 M314 E315 D316 W317 D320 K321 V322 K323 A324 H325 Y326 F329 T330 V331 Q332 N333 E334 A335 Y338 Q339 I340 N343 K344 Y345 R346 N351 A352 L353 M354 A357 S358 Q359 N364 M367 T368 I369 M373 S376 T377 T387 S388 G401 W402 W403 Y404 N405 R406 C407 A410 N411 P412 N413 G414 R415 G420 T423 W424 D425 M426 D432 D433 G434 V435 V436 W437 M438 N439 G442 S443 M447 R448 K449 M450 S451 M452 K453 I454 F457 F458 Molecule 3: Fibrinogen gamma chain Chain C: TYR CYS CYS ILE R14 Y18 C19 P20 T21 T22 C23 G24 I25 A26 D27 T31 Y32 Q33 D37 Q41 S42 L43 E44 D45 I46 L47 V50 V57 K58 A63 I64 Q65 L66 T67 Y68 N69 P70 D71 E72 S73 S74 K75 P76 N77 M78 I79 L84 K85 S86 L90 I93 Y96 E97 I100 L101 I107 L110 I113 N117 N118 Q119 K120 I121 V122 N123 L124 K125 E126 K127 V128 A129 Q130 L131 E132 A133 Q134 K140 V143 H146 D147 I148 K151 Q154 A157 N158 K159 G160 A161 K162 Q163 L166 Y167 F168 I169 A174 Q177 F178 L179 V180 Y181 C182 E183 W191 F194 Q195 K196 R197 L198 F204 K205 K206 N207 W208 I209 Q210 Y211 F215 G216 H217 L218 S219 P220 T221 T224 E225 F226 W227 L228 G229 N230 E231 K232 I233 H234 L235 I236 S237 T238 Q239 S240 A241 I242 P243 L246 R247 V248 E249 L250 E251 D252 W253 N254 G255 R256 T257 S258 T259 A260 D261 Y262 A263 M264 V267 G268 Y274 R275 L276 T277 Y278 A279 A282 A286 G287 D288 A289 F290 D291 G292 F293 D294 F295 S300 D301 K302 F303 F304 T305 S306 H307 Q311 D316 N317 D318 N325 G333 N337 K338 C339 H340 A341 G342 H343 L344 N345 G346 V347 Y348 Y349 Q350 G351 G352 T353 Y354 S355 K356 A357 S358 T359 G362 Y363 D364 N365 G366 I367 I368 W369 A370 T371 W372 K373 T374 R375 W376 Y377 S378 M379 K380 K381 T382 T383 M384 K385 I386 I387 P388 F389 N390 R391 L392 T393 I394
Page 18 Full wwpdb X-ray Structure Validation Report 3GHG Molecule 3: Fibrinogen gamma chain Chain F: C339 H340 A341 G342 H343 L344 N345 G346 Q350 G351 G352 T353 Y354 S355 K356 A357 S358 T359 P360 N361 N365 G366 I367 T371 R375 W376 Y377 S378 M379 K380 K381 T382 T383 M384 K385 I386 I387 R391 L392 T393 I394 G395 D252 W253 N254 T259 A260 D261 Y262 A263 M264 V267 G268 Y274 R275 Y278 F281 D285 A286 G287 D288 A289 G296 D297 D298 P299 S300 D301 T305 S306 H307 N308 G309 M310 S313 N317 E323 G324 N325 C326 A327 D330 G331 S332 G333 W334 W335 M336 N337 K338 I169 N175 F178 L179 V180 I184 D185 N189 G190 W191 T192 V193 F194 Q195 K196 R197 L198 D199 V202 D203 I209 Q210 Y211 G214 F215 G216 H217 L218 S219 P220 T224 E225 L228 G229 N230 I233 H234 L235 I236 S237 T238 I242 L246 R247 V248 E249 L250 E251 A82 K85 S86 R87 L90 E91 E92 I93 I100 L101 T102 H103 D104 I107 R108 Y109 L110 I113 Y114 N117 N118 Q119 K120 I121 V122 N123 L124 K125 E126 K127 V128 A129 Q130 Q136 K140 D141 T142 V143 D147 K151 D152 I156 A157 K162 L166 Y167 F168 TYR CYS CYS ILE R14 Y18 I25 A26 D27 T31 K35 I46 L47 H48 Q49 V50 E51 N52 K53 T54 S55 E56 Q59 L60 I61 K62 A63 I64 Q65 L66 T67 Y68 N69 P70 D71 E72 S73 S74 K75 P76 N77 M78 I79 D80 A81 Molecule 3: Fibrinogen gamma chain Chain I: L344 Y348 S355 K356 T359 P360 N361 G362 N365 G366 I367 I368 T371 W372 K373 W376 Y377 S378 M379 T382 T383 M384 K385 I386 I387 N390 R391 L392 T393 I394 G395 T259 A260 D261 K266 V267 G268 D272 R275 L276 T277 F281 A282 G283 G284 D285 A286 G287 D288 A289 D294 D297 F304 T305 S306 H307 M310 T314 N317 K321 F322 E323 G324 N325 C326 Q329 S332 G333 W334 W335 M336 N337 K338 C339 H340 A341 G342 H343 L179 V180 N189 G190 W191 T192 V193 F194 Q195 K196 R197 L198 D199 G200 S201 N207 W208 I209 G216 H217 L218 S219 P220 T223 T224 E225 F226 W227 L228 G229 N230 E231 K232 I233 H234 L235 I236 S237 T238 Q239 S240 A241 I242 R247 V248 E249 L250 E251 D252 W253 N254 T257 S258 S74 K75 P76 N77 M78 I79 D80 A81 A82 T83 L84 K85 S86 R87 K88 M89 L90 I93 A98 T102 H103 R108 Q111 E112 I113 Y114 N115 S116 N117 N118 Q119 K120 I121 V128 D141 T142 V143 Q144 I145 I148 T149 G150 K151 I156 L166 Y167 F168 I169 L172 TYR V2 A3 T4 R5 D6 N7 C8 C9 I10 L11 D12 E13 R14 F15 G16 S17 Y18 C19 P20 T21 T22 C23 G24 D27 F28 L29 S30 T31 Y32 Q33 V36 L40 Q41 S42 L43 I46 E51 N52 K53 T54 L60 A63 I64 Q65 L66 T67 Y68 N69 P70 D71 E72 S73 Molecule 3: Fibrinogen gamma chain Chain L: TYR R5 D6 N7 C8 C9 I10 L11 D12 E13 R14 S17 Y18 T21 T22 C23 G24 I25 A26 D27 L40 L43 E44 D45 I46 L47 H48 Q49 N52 K53 T54 S55 E56 V57 K58 A63 I64 Q65 L66 T67 Y68 N69 P70 D71 S74 K75 P76 N77 M78 I79
Page 19 Full wwpdb X-ray Structure Validation Report 3GHG P388 F389 N390 R391 G395 H307 T314 D318 N319 D320 N325 C326 A327 G331 W334 W335 M336 N337 K338 C339 H340 A341 G342 H343 L344 Y349 G352 T353 K356 T359 P360 N361 G362 Y363 D364 N365 G366 I367 T371 W372 K373 T374 R375 W376 Y377 S378 M379 K380 K381 T382 T383 M384 K385 I386 I387 I233 H234 L235 I236 S237 T238 Q239 I242 P243 Y244 A245 L246 R247 V248 E249 L250 E251 T259 A260 D261 M264 V267 E270 A271 D272 K273 Y274 R275 L276 T277 Y278 F281 A282 G283 A286 G287 D288 A289 F290 D291 F295 G296 D297 D298 P299 S300 D301 K302 F303 F304 T305 S306 L166 Y167 F168 I169 K170 P171 L172 K173 A174 N175 Q176 Q177 F178 L179 V180 I184 D185 N189 G190 W191 T192 V193 F194 Q195 K196 R197 L198 D199 D203 F204 K205 K206 N207 W208 I209 Q210 Y211 K212 E213 G214 H217 L218 S219 P220 T221 G222 T223 T224 E225 F226 W227 L228 G229 N230 E231 K232 D80 A81 A82 T83 L84 K85 S86 R87 L90 Y96 E97 I100 D104 I107 R108 Y109 L110 Q111 E112 I113 Y114 N115 S116 N117 K120 I121 V122 N123 L124 V128 C139 K140 D141 T142 V143 Q144 I145 H146 D147 I148 T149 G150 K151 D152 C153 Q154 D155 I156 A157 Q163 Molecule 4: A knob Chain M: G1 P2 R3 P4 Molecule 4: A knob Chain N: G1 P2 R3 P4 Molecule 4: A knob Chain Q: G1 P2 R3 P4 Molecule 4: A knob Chain R: G1 P2 R3 P4 Molecule 5: B knob Chain O: G1 H2 R3 P4 Molecule 5: B knob Chain P:
Page 20 Full wwpdb X-ray Structure Validation Report 3GHG G1 H2 R3 P4 Molecule 5: B knob Chain S: G1 H2 R3 P4 Molecule 5: B knob Chain T: G1 H2 R3 P4
Page 21 Full wwpdb X-ray Structure Validation Report 3GHG 4 Data and refinement statistics i Property Value Source Space group P 1 21 1 Depositor Cell constants 135.24Å 94.87Å 300.81Å a, b, c, α, β, γ 90.00 94.81 90.00 Depositor Resolution (Å) 19.95 2.90 Depositor 19.93 2.90 EDS % Data completeness (in resolution range) 100.0 (19.95-2.90) 69.4 (19.93-2.90) Depositor EDS R merge (Not available) Depositor R sym 0.10 Depositor < I/σ(I) > 1 3.46 (at 2.88Å) Xtriage Refinement program REFMAC 5.4.0061 Depositor 0.252, 0.309 Depositor R, R free 0.259, 0.311 DCC R free test set 5820 reflections (5.00%) wwpdb-vp Wilson B-factor (Å 2 ) 84.4 Xtriage Anisotropy 0.103 Xtriage Bulk solvent k sol (e/å 3 ), B sol (Å 2 ) 0.20, 75.5 EDS L-test for twinning 2 < L > = 0.43, < L 2 > = 0.25 Xtriage Estimated twinning fraction No twinning to report. Xtriage F o,f c correlation 0.92 EDS Total number of atoms 31833 wwpdb-vp Average B, all atoms (Å 2 ) 90.0 wwpdb-vp Xtriage s analysis on translational NCS is as follows: The analyses of the Patterson function reveals a significant off-origin peak that is 30.84 % of the origin peak, indicating pseudo-translational symmetry. The chance of finding a peak of this or larger height randomly in a structure without pseudo-translational symmetry is equal to 1.2228e-03. The detected translational NCS is most likely also responsible for the elevated intensity ratio. 1 Intensities estimated from amplitudes. 2 Theoretical values of < L >, < L 2 > for acentric reflections are 0.5, 0.333 respectively for untwinned datasets, and 0.375, 0.2 for perfectly twinned datasets.
Page 22 Full wwpdb X-ray Structure Validation Report 3GHG 5 Model quality i 5.1 Standard geometry i Bond lengths and bond angles in the following residue types are not validated in this section: BMA, NAG, CA, NDG, SIA, GAL, MAN 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 A 0.45 0/1447 0.61 0/1939 1 D 0.44 0/1447 0.56 0/1939 1 G 0.40 0/1447 0.54 0/1939 1 J 0.46 0/1547 0.62 0/2076 2 B 0.59 0/3283 0.73 0/4438 2 E 0.52 0/3283 0.62 0/4438 2 H 0.52 0/3283 0.65 0/4438 2 K 0.51 0/3283 0.65 0/4438 3 C 0.83 2/3125 (0.1%) 0.84 2/4224 (0.0%) 3 F 0.46 0/3129 0.57 1/4229 (0.0%) 3 I 0.53 0/3220 0.63 0/4353 3 L 0.55 0/3201 0.65 0/4326 4 M 0.80 0/31 0.89 0/40 4 N 0.46 0/31 0.62 0/40 4 Q 0.74 0/31 0.62 0/40 4 R 0.74 0/31 0.59 0/40 5 O 0.57 0/34 0.72 0/43 5 P 0.48 0/34 0.67 0/43 5 S 0.47 0/34 0.59 0/43 5 T 0.56 0/34 0.86 0/43 All All 0.55 2/31955 (0.0%) 0.66 3/43109 (0.0%) All (2) bond length outliers are listed below: Mol Chain Res Type Atoms Z Observed(Å) Ideal(Å) 3 C 181 TYR CG-CD1-5.83 1.31 1.39 3 C 181 TYR CG-CD2-5.10 1.32 1.39 All (3) bond angle outliers are listed below:
Page 23 Full wwpdb X-ray Structure Validation Report 3GHG Mol Chain Res Type Atoms Z Observed( o ) Ideal( o ) 3 F 90 CA-CB-CG 5.60 128.18 115.30 3 C 364 CB-CG-OD1 5.47 123.22 118.30 3 C 363 TYR CA-CB-CG 5.25 123.38 113.40 There are no chirality outliers. There are no planarity outliers. 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 1431 0 1424 104 0 1 D 1431 0 1424 72 0 1 G 1431 0 1424 78 0 1 J 1527 0 1533 140 1 2 B 3209 0 3042 210 0 2 E 3209 0 3042 181 0 2 H 3209 0 3041 159 0 2 K 3209 0 3043 192 0 3 C 3050 0 2906 209 0 3 F 3054 0 2909 157 0 3 I 3145 0 2993 186 1 3 L 3126 0 2972 239 0 4 M 30 0 32 2 0 4 N 30 0 32 0 0 4 Q 30 0 32 0 0 4 R 30 0 32 1 0 5 O 33 0 32 3 0 5 P 33 0 32 2 0 5 S 33 0 32 4 0 5 T 33 0 32 4 0 6 B 14 0 12 9 0 6 E 14 0 12 2 0 6 H 14 0 12 5 0 6 K 14 0 12 7 0 6 L 28 0 25 12 0 7 B 42 0 36 12 0 7 E 42 0 36 7 0
Page 24 Full wwpdb X-ray Structure Validation Report 3GHG Mol Chain Non-H H(model) H(added) Clashes Symm-Clashes 7 H 14 0 12 4 0 7 K 42 0 36 8 0 8 B 11 0 8 3 0 8 E 11 0 8 4 0 8 H 11 0 8 2 0 8 K 11 0 8 2 0 9 B 22 0 18 4 0 9 E 22 0 18 3 0 9 H 22 0 20 0 0 9 K 22 0 18 2 0 10 B 22 0 18 5 0 10 E 22 0 18 3 0 10 K 22 0 18 2 0 11 B 40 0 34 6 0 11 E 40 0 34 6 0 11 K 40 0 34 4 0 12 B 1 0 0 0 0 12 C 1 0 0 0 0 12 E 1 0 0 0 0 12 F 1 0 0 0 0 12 H 1 0 0 0 0 12 I 1 0 0 0 0 12 K 1 0 0 0 0 12 L 1 0 0 0 0 All All 31833 0 30464 1667 1 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 27. All (1667) 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) 2:K:364::HD21 6:K:470:NAG:C1 1.17 1.55 2:B:364::ND2 6:B:470:NAG:C1 1.70 1.52 2:K:364::ND2 6:K:470:NAG:C1 1.85 1.38 3:L:56::HB2 6:L:570:NAG:O3 1.20 1.32 2:H:172::HD21 3:I:113:ILE:CG2 1.70 1.19 1:J:108:TYR:OH 3:L:83::C 1.85 1.15 1:J:115::CD2 3:L:90::HD21 1.78 1.14 1:A:115::HD21 3:C:90::HD13 1.23 1.13 3:I:10:ILE:O 3:I:18:TYR:OH 1.65 1.12
Page 25 Full wwpdb X-ray Structure Validation Report 3GHG Atom-1 Atom-2 Interatomic Clash distance (Å) overlap (Å) 2:K:302::HD22 2:K:454:ILE:HD11 1.31 1.11 1:G:108:TYR:CE2 3:I:82::HB1 1.86 1.11 3:I:12::HB3 3:I:15::HD1 0.99 1.09 3:I:12::CB 3:I:15::HD1 1.65 1.08 7:K:471:NDG:H6C2 7:K:477:NDG:H8C2 1.17 1.07 1:G:154:ILE:HD11 3:I:128::HG21 1.28 1.07 1:J:108:TYR:OH 3:L:84::N 1.87 1.07 3:I:12::HB3 3:I:15::CD1 1.90 1.06 1:A:55:ILE:HG23 2:B:86::HD21 1.35 1.06 3:I:27::O 3:I:31::HG23 1.56 1.06 1:J:115::HD21 3:L:90::HD21 1.12 1.06 1:A:108:TYR:O 1:A:112::OG 1.74 1.05 3:F:260::HB2 3:F:286::HB3 1.34 1.04 3:L:49::NE2 6:L:570:NAG:H81 1.72 1.02 3:L:359::HG21 3:L:363:TYR:O 1.59 1.02 1:G:119:ILE:HD11 3:I:93:ILE:CD1 1.89 1.01 1:A:119:ILE:HD13 3:C:93:ILE:HD13 1.43 1.01 2:B:252:ILE:HD11 2:B:454:ILE:HD13 1.02 1.01 2:H:172::HD21 3:I:113:ILE:HG21 1.39 1.01 3:L:52::ND2 6:L:570:NAG:C1 2.24 1.01 1:G:154:ILE:CD1 3:I:128::HG21 1.90 0.99 1:D:135::HD22 1:D:136::HD22 1.43 0.99 1:G:105::OD1 3:I:79:ILE:HD11 1.63 0.98 2:B:154::OD1 3:C:96:TYR:OH 1.79 0.98 1:J:60::O 1:J:64::OD1 1.81 0.98 1:A:115::CD2 3:C:90::HD13 1.94 0.97 1:J:207:MET:HB2 2:K:135::HD21 1.21 0.97 1:J:108:TYR:CE1 3:L:83::HB 1.99 0.97 1:G:55:ILE:HD12 2:H:82::HD22 1.44 0.97 3:I:8:CYS:SG 3:I:18:TYR:CD2 2.58 0.97 3:I:8:CYS:SG 3:I:18:TYR:CE2 2.58 0.97 1:G:119:ILE:HD11 3:I:93:ILE:HD11 1.48 0.95 3:L:56::HB2 6:L:570:NAG:HO3 1.21 0.95 3:L:219::H 3:L:224::HG21 1.29 0.95 2:B:159::O 2:B:163::HG23 1.67 0.95 3:L:56::CB 6:L:570:NAG:O3 2.15 0.94 2:E:241::OD1 2:E:244::OG1 1.85 0.94 1:J:115::HD13 3:L:90::HD11 1.50 0.93 2:B:252:ILE:HD11 2:B:454:ILE:CD1 1.97 0.93 2:E:312:ILE:HB 2:E:324::HB3 1.51 0.92 2:H:310::HD12 2:H:311::N 1.85 0.92
Page 26 Full wwpdb X-ray Structure Validation Report 3GHG Atom-1 Atom-2 Interatomic Clash distance (Å) overlap (Å) 2:E:222::OG 2:E:242:MET:N 2.01 0.92 2:H:252:ILE:HD12 2:H:454:ILE:HG23 1.50 0.92 2:B:239:TYR:OH 2:B:287::O 1.85 0.91 2:B:230::O 2:B:233::HG12 1.69 0.91 3:I:12::CB 3:I:15::CD1 2.51 0.90 3:C:390::HD22 3:C:391::N 1.69 0.90 1:J:115::HD21 3:L:90::CD2 2.00 0.90 2:B:252:ILE:CD1 2:B:454:ILE:HD13 1.96 0.89 3:F:323::N 3:F:323::OE2 2.05 0.89 2:H:172::CD2 3:I:113:ILE:HG21 2.02 0.89 3:C:307::HE1 3:C:342::H 1.21 0.88 3:L:52::ND2 6:L:570:NAG:O5 2.07 0.88 1:A:55:ILE:HD12 2:B:82::HD22 1.53 0.88 1:A:144::HD13 2:B:175::HD11 1.54 0.88 1:J:108:TYR:HH 3:L:84::N 1.69 0.88 2:B:172::HB3 3:C:113:ILE:HG21 1.57 0.87 2:H:135::O 2:H:139::HG23 1.74 0.87 1:J:184::HE21 2:K:167::HG23 1.37 0.87 3:L:219::OG 3:L:224::HG22 1.74 0.86 2:K:201:CYS:O 3:L:143::HG21 1.74 0.86 1:A:55:ILE:HG23 2:B:86::CD2 2.04 0.85 1:J:169::HB2 2:K:189::HE22 1.41 0.85 1:J:148::HZ1 2:K:425::CG 1.79 0.85 2:E:222::HG 2:E:242:MET:H 1.19 0.85 3:I:219::OG 3:I:224::HG22 1.77 0.85 3:L:49::NE2 6:L:570:NAG:C8 2.39 0.85 2:H:210::OE2 2:H:212::N 2.09 0.84 1:J:69::HD11 2:K:100::HD13 1.56 0.84 1:A:122::HD11 2:B:153:ILE:HG21 1.60 0.83 1:A:73::HD23 2:B:104::HG22 1.60 0.83 3:F:246::HD11 3:F:248::HG23 1.59 0.83 2:H:172::HD21 3:I:113:ILE:CB 2.08 0.83 2:E:172::CD2 3:F:113:ILE:HG23 2.07 0.83 2:B:373:MET:HG3 2:B:405::HB2 1.61 0.83 2:H:302::HD22 2:H:454:ILE:CD1 2.09 0.82 2:K:310::HD12 2:K:311::N 1.94 0.82 3:L:52::HD22 6:L:570:NAG:C1 1.91 0.82 3:C:194::CD1 3:C:233:ILE:CD1 2.63 0.82 2:B:364::CG 6:B:470:NAG:C1 2.46 0.82 1:A:59::HD21 2:B:86::HD23 1.41 0.82 2:H:252:ILE:HD11 2:H:454:ILE:HD13 1.60 0.82
Page 27 Full wwpdb X-ray Structure Validation Report 3GHG Atom-1 Atom-2 Interatomic Clash distance (Å) overlap (Å) 1:J:207:MET:HB2 2:K:135::ND2 1.95 0.82 2:K:133::O 2:K:136::HG2 1.79 0.82 2:K:343::HA 2:K:354:MET:SD 2.21 0.81 1:J:115::HD13 3:L:90::CD1 2.11 0.80 2:E:212::O 2:E:215:ILE:HG22 1.81 0.80 3:C:254::N 3:C:254::HD22 1.79 0.80 2:H:310::HD12 2:H:311::H 1.46 0.80 2:K:423::OG1 2:K:425::OD1 1.99 0.80 1:A:123::HA 1:A:126::HG12 1.62 0.80 1:G:93:ILE:HG22 1:G:94::HD12 1.62 0.80 3:C:215::CE2 3:C:227:TRP:HB3 2.17 0.80 3:C:179::HD22 3:C:218::HD13 1.63 0.79 3:F:234::ND1 3:F:267::O 2.11 0.79 3:I:208:TRP:HA 3:I:314::HG21 1.64 0.79 2:B:354:MET:O 2:B:369:ILE:HD13 1.81 0.79 1:D:119:ILE:HD11 3:F:93:ILE:HD13 1.64 0.79 3:C:253:TRP:C 3:C:254::HD22 1.85 0.79 2:E:397::HB3 2:E:431::HG21 1.62 0.79 2:H:252:ILE:CD1 2:H:454:ILE:HG23 2.12 0.79 2:K:295::O 2:K:299:ILE:HG13 1.83 0.79 7:K:471:NDG:H6C2 7:K:477:NDG:C8 2.09 0.79 3:F:46:ILE:O 3:F:50::HG22 1.83 0.79 1:A:119:ILE:HD13 3:C:93:ILE:CD1 2.14 0.78 3:C:307::CE1 3:C:342::H 2.02 0.78 1:G:58::HG21 3:I:29::HD11 1.66 0.78 2:B:179:ILE:HG23 2:B:180::N 1.98 0.78 1:J:108:TYR:CZ 3:L:83::HB 2.18 0.78 1:J:205:ILE:HG13 2:K:138::HG11 1.65 0.78 2:B:351::C 2:B:351::HD22 1.87 0.78 2:E:343::HA 2:E:354:MET:SD 2.24 0.78 1:A:69::HD12 2:B:100::HD13 1.67 0.77 2:E:326:TYR:CE1 2:E:353::HD12 2.19 0.77 2:E:165::HD21 3:F:107:ILE:HD12 1.64 0.77 1:A:71::HD22 1:A:72::N 1.82 0.77 3:F:296::N 3:F:301::OD2 2.18 0.77 2:B:252:ILE:HD12 2:B:454:ILE:HG23 1.67 0.77 1:J:46::O 3:L:22::HG21 1.85 0.77 2:E:203:ILE:HG22 2:E:204::O 1.85 0.77 2:H:78::HG23 1:J:43:TYR:O 1.84 0.76 2:K:210::OE2 2:K:212::N 2.14 0.76 2:B:165::HD11 3:C:107:ILE:CD1 2.15 0.76
Page 28 Full wwpdb X-ray Structure Validation Report 3GHG Atom-1 Atom-2 Interatomic Clash distance (Å) overlap (Å) 3:I:8:CYS:SG 3:I:18:TYR:HD2 2.06 0.76 1:A:55:ILE:CD1 2:B:82::HD22 2.16 0.76 3:C:246::HD21 3:C:248::CG2 2.16 0.76 3:C:364::O 3:C:364::OD1 2.04 0.76 3:I:281::CE2 3:I:283::HA2 2.20 0.76 3:I:8:CYS:SG 3:I:18:TYR:HE2 2.06 0.76 3:F:246::HD12 3:F:247::N 2.00 0.76 3:I:143::O 3:I:143::HG23 1.84 0.76 2:K:312:ILE:HB 2:K:324::HB3 1.67 0.76 1:A:122::HD11 2:B:153:ILE:CG2 2.16 0.76 2:H:434::O 2:H:436::HG23 1.85 0.75 3:I:260::HB2 3:I:286::HB3 1.66 0.75 1:J:63::HA 1:J:66:ILE:HG22 1.68 0.75 1:G:69::HD12 2:H:100::HD13 1.68 0.75 2:K:149::C 2:K:149::ND1 2.39 0.75 3:L:246::HD12 3:L:247::N 2.02 0.75 3:F:90::HD22 3:F:91::N 2.02 0.75 2:B:320::OD2 2:B:320::N 2.16 0.74 2:K:252:ILE:HD12 2:K:452:MET:C 2.08 0.74 1:A:122::CD1 2:B:153:ILE:HG21 2.17 0.74 3:L:77::HA 3:L:82::HB2 1.69 0.74 2:H:367:MET:SD 2:H:406::HD3 2.28 0.74 1:J:69::HD13 1:J:69::C 2.08 0.74 3:C:90::O 3:C:93:ILE:HG22 1.87 0.74 3:I:207::HD21 3:I:209:ILE:HD13 1.51 0.74 1:J:128::O 1:J:132::ND1 2.21 0.74 2:K:439::HD22 2:K:439::N 1.86 0.74 2:B:205::O 2:B:205::HG12 1.87 0.73 2:E:181::O 2:E:185::HB2 1.87 0.73 3:I:141::CG 3:I:143::HG22 2.07 0.73 3:L:198::HD13 3:L:199::N 2.02 0.73 1:D:55:ILE:HG23 2:E:86::HD13 1.69 0.73 2:B:381::HB2 2:B:393::HE21 1.54 0.73 2:B:169::HA 3:C:110::HD21 1.69 0.73 1:J:66:ILE:HG23 1:J:67::HD22 1.54 0.73 2:K:412::HG3 2:K:450:MET:HE3 1.71 0.73 6:K:470:NAG:O3 7:K:471:NDG:H2 1.90 0.72 2:H:172::CD2 3:I:113:ILE:CG2 2.58 0.72 2:H:59::HB1 2:H:60::HD2 1.70 0.72 2:H:201:CYS:O 3:I:143::HG21 1.88 0.72 3:C:368:ILE:CG2 3:C:377:TYR:O 2.37 0.72
Page 29 Full wwpdb X-ray Structure Validation Report 3GHG Atom-1 Atom-2 Interatomic Clash distance (Å) overlap (Å) 3:F:218::N 3:F:218::HD23 2.04 0.72 3:I:219::OG 3:I:224::CG2 2.37 0.72 3:L:203::O 3:L:206::NZ 2.23 0.72 1:D:86::HD23 3:F:61:ILE:HD12 1.71 0.72 3:C:249::HB3 3:C:383::HG23 1.72 0.71 2:K:364::ND2 6:K:470:NAG:C2 2.52 0.71 3:L:334:TRP:HH2 3:L:344::HD12 1.54 0.71 1:J:129::O 1:J:133:ILE:HD13 1.91 0.71 2:K:172::HD22 3:L:113:ILE:HG23 1.70 0.71 3:L:344::HA 3:L:367:ILE:HG23 1.72 0.71 3:L:213::O 3:L:232::NZ 2.20 0.71 1:J:127:ILE:HA 1:J:130::HG12 1.70 0.71 3:L:318::OD1 3:L:325::ND2 2.22 0.71 3:C:194::CD1 3:C:233:ILE:HD13 2.25 0.71 3:C:295::CE1 3:C:305::HG21 2.25 0.71 1:J:148::NZ 2:K:425::CG 2.42 0.71 1:J:169::HB2 2:K:189::NE2 2.06 0.71 2:E:316::OD2 2:E:320::N 2.23 0.71 2:E:406::H 2:E:407:CYS:HA 1.56 0.71 3:F:301::O 3:F:305::HG23 1.89 0.71 1:J:67::HA 1:J:70::HE2 1.73 0.71 1:A:175::HD12 2:B:426:MET:CE 2.21 0.70 1:G:55:ILE:CD1 2:H:82::HD22 2.20 0.70 2:K:149::ND1 2:K:150::N 2.39 0.70 3:C:194::CG 3:C:233:ILE:HD13 2.27 0.70 3:I:3::HB2 3:L:11::HD12 1.73 0.70 3:F:147::OD1 3:F:147::N 2.23 0.70 2:H:302::HD22 2:H:454:ILE:HD11 1.73 0.70 1:G:123::HA 1:G:126::HG12 1.72 0.70 1:A:71::C 1:A:71::HD22 1.95 0.70 3:L:195::NE2 3:L:197::HG3 2.06 0.70 2:E:169::HA 3:F:110::HD11 1.74 0.70 3:F:169:ILE:HD11 3:F:180::HG21 1.74 0.70 3:C:75::HB3 3:C:78:MET:HE3 1.72 0.70 1:A:129::O 1:A:133:ILE:HD13 1.91 0.70 3:C:276::C 3:C:276::HD23 2.12 0.70 3:L:9:CYS:O 3:L:17::HA 1.92 0.70 2:B:101::OD1 3:C:43::HD21 1.92 0.69 6:H:470:NAG:H62 5:S:4::HB3 1.73 0.69 2:B:364::HD22 6:B:470:NAG:C1 1.96 0.69 3:C:100:ILE:HG23 3:C:101::HD23 1.74 0.69
Page 30 Full wwpdb X-ray Structure Validation Report 3GHG Atom-1 Atom-2 Interatomic Clash distance (Å) overlap (Å) 1:A:119:ILE:CD1 3:C:93:ILE:HD13 2.18 0.69 2:E:168::HD22 3:F:110::CD2 2.21 0.69 2:K:118:MET:O 2:K:122::HB3 1.93 0.69 3:L:219::OG 3:L:224::CG2 2.38 0.69 1:A:59::HD21 2:B:86::CD2 2.05 0.69 1:D:118::HH22 3:F:90::HD23 1.56 0.69 2:E:351::HD21 2:E:354:MET:H 1.39 0.69 1:J:207:MET:O 1:J:211::HD3 1.93 0.69 2:H:224:MET:HE2 2:H:237::HD3 1.75 0.69 3:I:81::O 3:I:85::N 2.23 0.69 11:B:479:SIA:H7 11:B:479:SIA:O10 1.93 0.69 3:C:368:ILE:HG22 3:C:377:TYR:O 1.92 0.69 2:K:179:ILE:HD11 3:L:121:ILE:HG13 1.75 0.69 1:J:115::O 1:J:119:ILE:HG12 1.93 0.69 2:B:253::C 2:B:253::HE21 1.96 0.69 1:A:111::O 1:A:115::HD12 1.93 0.69 10:B:476:GAL:H5 11:B:480:SIA:H32 1.74 0.69 3:F:246::HD11 3:F:248::CG2 2.23 0.68 1:J:71::HA 1:J:74::CD2 2.28 0.68 2:B:252:ILE:CD1 2:B:454:ILE:HG23 2.23 0.68 3:C:166::HB3 3:C:179::HD21 1.75 0.68 3:C:197::NH1 3:C:367:ILE:HD11 2.08 0.68 2:H:342::HG11 2:H:353::HD13 1.74 0.68 1:J:145::HG13 1:J:146::N 2.07 0.68 2:K:212::O 2:K:215:ILE:HG22 1.92 0.68 2:K:432::OD1 2:K:443::OG 2.10 0.68 3:C:248::HG12 3:C:250::HD11 1.73 0.68 1:A:115::HD21 3:C:90::CD1 2.14 0.68 2:E:436::HG11 2:E:443::HA 1.75 0.68 1:G:115::HD11 3:I:89:MET:HB2 1.75 0.68 3:F:27::O 3:F:31::HB 1.94 0.68 2:K:345:TYR:HB2 2:K:354:MET:HE2 1.74 0.68 1:A:63::HA 1:A:66:ILE:HG22 1.75 0.68 3:C:291::O 3:C:302::NZ 2.27 0.68 3:F:260::HB2 3:F:286::CB 2.20 0.67 2:H:172::HD21 3:I:113:ILE:HB 1.75 0.67 1:J:144::HD22 2:K:171:ILE:HD11 1.75 0.67 1:J:121::HG12 1:J:122::HD22 1.74 0.67 1:J:69::HD11 2:K:100::CD1 2.24 0.67 2:K:102::O 2:K:106::HB3 1.94 0.67 3:L:379:MET:HE3 3:L:379:MET:HA 1.75 0.67
Page 31 Full wwpdb X-ray Structure Validation Report 3GHG Atom-1 Atom-2 Interatomic Clash distance (Å) overlap (Å) 2:B:406::N 2:B:407:CYS:HA 2.08 0.67 1:D:55:ILE:CG2 2:E:86::HD13 2.24 0.67 3:L:314::C 3:L:327::HB1 2.15 0.67 3:L:288::C 3:L:371::HG21 2.14 0.67 2:B:408::O 5:O:1::N 2.24 0.67 3:C:350::O 3:C:352::N 2.21 0.67 2:K:364::CG 6:K:470:NAG:C1 2.61 0.67 1:A:115::HD11 3:C:90::HB2 1.76 0.67 3:C:181:TYR:HE1 3:C:220::O 1.77 0.67 1:A:175::HD12 2:B:426:MET:HE2 1.76 0.67 2:H:398::HA 2:H:433::HB3 1.77 0.67 2:H:135::HA 2:H:138::HG12 1.77 0.67 3:I:79:ILE:HA 3:I:82::HB3 1.76 0.67 3:I:199::OD1 3:I:201::N 2.27 0.66 2:K:351::HD21 2:K:354:MET:HG3 1.59 0.66 2:B:367:MET:SD 2:B:406::HD3 2.35 0.66 3:C:225::O 3:C:226::HB3 1.96 0.66 2:H:361:MET:HB2 6:H:470:NAG:H81 1.78 0.66 3:L:185::OD2 3:L:189::N 2.25 0.66 2:H:360::HD11 5:S:2::ND1 2.10 0.66 3:I:11::HD23 3:I:12::N 2.11 0.66 7:B:477:NDG:H4 10:B:478:GAL:O2 1.95 0.66 3:C:276::HD21 3:C:278:TYR:CD2 2.31 0.66 2:E:406::N 2:E:407:CYS:HA 2.10 0.66 3:L:242:ILE:HG23 3:L:243::HD2 1.76 0.66 7:B:471:NDG:O6 7:B:477:NDG:H2 1.94 0.66 3:C:365::H 3:C:365::HD22 1.43 0.66 3:C:194::CD1 3:C:233:ILE:HD11 2.29 0.66 1:J:208::HB2 1:J:209::HD3 1.78 0.66 1:J:51:MET:HG3 3:L:22::HG22 1.77 0.66 3:L:11::HB3 3:L:18:TYR:CE1 2.31 0.66 3:C:179::HD23 3:C:180::N 2.10 0.66 3:C:364::OD2 4:M:1::N 2.28 0.66 1:G:119:ILE:HD11 3:I:93:ILE:HD13 1.78 0.66 1:D:109::OD1 1:D:110::N 2.29 0.65 2:H:182::O 2:H:185::N 2.29 0.65 2:B:294::HD12 2:B:295::H 1.62 0.65 2:H:257::OD1 2:H:259::OG 2.10 0.65 3:F:27::O 3:F:31::CB 2.45 0.65 1:G:123::NZ 2:H:153:ILE:HG21 2.10 0.65 2:B:354:MET:O 2:B:369:ILE:HG23 1.96 0.65
Page 32 Full wwpdb X-ray Structure Validation Report 3GHG Atom-1 Atom-2 Interatomic Clash distance (Å) overlap (Å) 3:C:197::HD2 3:C:344::O 1.97 0.65 2:E:340:ILE:HD12 2:E:403:TRP:CZ3 2.31 0.65 2:H:302::HD22 2:H:454:ILE:HD12 1.77 0.65 3:I:42::O 3:I:46:ILE:HD13 1.96 0.65 3:L:236:ILE:HG21 3:L:386:ILE:HD11 1.77 0.65 3:L:264:MET:O 3:L:278:TYR:HA 1.96 0.65 6:L:570:NAG:H62 6:L:571:NAG:H61 1.77 0.65 9:B:473:MAN:H4 7:B:475:NDG:N2 2.12 0.65 2:K:276::HA 2:K:292:TYR:CD2 2.32 0.65 2:E:205::HG22 3:F:218::HD21 1.78 0.65 3:I:193::HG22 3:I:385::HB3 1.77 0.65 3:C:146::HD2 3:C:167:TYR:CZ 2.14 0.64 1:D:144::HD21 1:D:182::HA 1.78 0.64 3:L:169:ILE:CD1 3:L:180::HG11 2.27 0.64 1:A:134::NE2 1:A:193::HD23 2.12 0.64 2:E:296::O 2:E:299:ILE:N 2.28 0.64 2:H:252:ILE:CD1 2:H:454:ILE:CG2 2.75 0.64 2:B:154::CG 3:C:96:TYR:OH 2.34 0.64 2:E:227:ILE:HD11 2:E:236:TYR:CE2 2.33 0.64 2:E:326:TYR:OH 2:E:351::ND2 2.31 0.64 2:H:316::OD2 2:H:320::N 2.20 0.64 3:L:246::HD12 3:L:247::H 1.63 0.64 3:L:219::N 3:L:224::HG21 2.09 0.64 2:B:171:ILE:HG22 2:B:172::HD13 1.80 0.64 2:B:205::HG22 3:C:218::HG 1.79 0.64 1:J:69::HD13 1:J:70::N 2.13 0.64 6:B:470:NAG:O3 7:B:471:NDG:H2 1.98 0.64 2:E:160::O 2:E:164::N 2.20 0.64 7:H:471:NDG:H3 7:H:471:NDG:O7 1.98 0.64 2:H:66::N 1:J:34::O 2.31 0.64 1:J:71::HA 1:J:74::CE2 2.33 0.64 3:L:152::OD1 3:L:155::N 2.30 0.64 1:G:97::O 1:G:101::CB 2.46 0.64 2:B:165::HD11 3:C:107:ILE:HD12 1.79 0.64 3:C:365::N 3:C:365::HD22 1.96 0.64 3:C:174::HB2 3:C:235::HD13 1.79 0.63 3:C:340::ND1 3:C:340::O 2.30 0.63 2:E:199::O 3:F:141::OD2 2.16 0.63 3:L:209:ILE:H 3:L:209:ILE:HD12 1.63 0.63 3:F:250::HD23 3:F:379:MET:CE 2.28 0.63 2:H:153:ILE:HG22 2:H:153:ILE:O 1.97 0.63
Page 33 Full wwpdb X-ray Structure Validation Report 3GHG Atom-1 Atom-2 Interatomic Clash distance (Å) overlap (Å) 3:I:189::HB3 3:I:387:ILE:HD11 1.78 0.63 1:A:134::HE22 1:A:193::HD23 1.63 0.63 1:A:169::HD23 1:A:171::HD2 1.80 0.63 3:I:5::HB2 3:I:11::HD13 1.80 0.63 2:K:199::HG23 3:L:141::HA 1.80 0.63 3:I:12::OD2 3:I:15::CD1 2.52 0.63 1:J:132::CB 3:L:107:ILE:HD11 2.28 0.63 2:K:332::O 2:K:338:TYR:HA 1.98 0.63 3:L:197::NH1 3:L:367:ILE:HD11 2.14 0.63 2:B:238::HG11 2:B:250::HG23 1.81 0.63 3:C:121:ILE:HG22 3:C:122::N 2.12 0.63 3:C:261::HB3 3:C:282::HB3 1.81 0.63 2:E:172::HD21 3:F:113:ILE:HG23 1.79 0.63 2:E:314:MET:CG 2:E:322::HG23 2.28 0.63 2:K:436::HG11 2:K:442::O 1.99 0.63 2:B:172::HB3 3:C:113:ILE:CG2 2.27 0.63 1:D:50::HD3 2:E:59::HB1 1.81 0.63 1:G:118::NH2 3:I:90::HD21 2.14 0.63 3:I:356::HA 3:I:359::HG23 1.80 0.63 1:G:184::HE21 2:H:167::HG23 1.64 0.62 3:I:242:ILE:O 3:I:242:ILE:HD12 1.98 0.62 2:B:281::O 2:B:281::OD2 2.18 0.62 7:B:477:NDG:H8C1 7:B:477:NDG:H3 1.81 0.62 2:E:226::HD11 2:E:235::HB2 1.80 0.62 2:E:385:TRP:O 2:E:387::N 2.29 0.62 1:J:115::CD2 3:L:90::CD2 2.66 0.62 2:K:172::CD2 3:L:113:ILE:HG23 2.29 0.62 3:C:246::HA 3:C:386:ILE:HG22 1.80 0.62 3:C:349:TYR:CE1 3:C:354:TYR:CE1 2.88 0.62 2:H:87::HD23 2:H:87::O 2.00 0.62 1:G:62::CE1 3:I:36::HG12 2.35 0.62 1:J:137::O 1:J:140::HG22 1.99 0.62 1:J:156:ILE:O 1:J:159::N 2.32 0.62 2:K:373:MET:SD 2:K:405::HB2 2.38 0.62 2:K:406::N 2:K:407:CYS:HA 2.13 0.62 1:D:118::NH2 3:F:90::HD23 2.13 0.62 1:D:86::CD2 3:F:61:ILE:HG21 2.30 0.62 2:E:171:ILE:CG2 2:E:172::N 2.62 0.62 2:E:205::HG23 3:F:216::O 1.98 0.62 3:I:169:ILE:HD11 3:I:180::HG11 1.80 0.62 2:K:376::O 2:K:401::HA2 1.99 0.62
Page 34 Full wwpdb X-ray Structure Validation Report 3GHG Atom-1 Atom-2 Interatomic Clash distance (Å) overlap (Å) 3:C:248::HG12 3:C:250::CD1 2.29 0.62 3:C:261::CB 3:C:282::HB3 2.30 0.61 2:H:171:ILE:HG23 2:H:172::N 2.15 0.61 1:J:106::ND2 1:J:106::C 2.54 0.61 3:C:333::O 3:C:345::ND2 2.32 0.61 2:E:340:ILE:HD12 2:E:403:TRP:CE3 2.36 0.61 1:J:154:ILE:HD11 3:L:128::HG21 1.80 0.61 3:C:295::HE1 3:C:305::HG21 1.63 0.61 2:E:165::HD21 3:F:107:ILE:CD1 2.30 0.61 2:H:122::HZ3 3:I:60::HB3 1.66 0.61 2:K:326:TYR:CE1 2:K:353::HD12 2.35 0.61 1:D:137::O 1:D:140::HG22 1.99 0.61 2:B:102::O 2:B:106::HB3 2.00 0.61 3:F:124::O 3:F:128::HG23 1.99 0.61 2:K:137::HA 2:K:140::HD21 1.64 0.61 3:C:240::O 3:C:242:ILE:N 2.28 0.61 1:G:185::HD11 1:G:189:ILE:HD11 1.82 0.61 2:H:253::C 2:H:253::HE21 2.03 0.61 2:B:172::HD22 3:C:110::HD22 1.81 0.61 2:E:176::O 2:E:179:ILE:HG22 2.01 0.61 3:L:56::CB 6:L:570:NAG:HO3 2.03 0.61 1:D:135::HD22 1:D:136::CD2 2.24 0.61 3:I:116::O 3:I:119::N 2.33 0.61 3:I:141::OD2 3:I:143::HG22 2.01 0.61 2:K:410::HB1 2:K:437:TRP:CE3 2.36 0.61 1:J:118::O 1:J:122::HD23 2.01 0.61 2:E:226::HD11 2:E:235::CB 2.30 0.60 2:E:199::HG23 3:F:141::HA 1.82 0.60 2:H:75::HD22 1:J:46::N 2.16 0.60 1:J:63::HA 1:J:66:ILE:CG2 2.31 0.60 3:L:143::HG23 3:L:143::O 2.00 0.60 2:B:260::HG21 2:B:291::O 2.01 0.60 2:E:312:ILE:HD11 2:E:452:MET:HE2 1.83 0.60 3:F:191:TRP:CE3 3:F:385::HG3 2.35 0.60 1:G:154:ILE:HD11 3:I:128::CG2 2.19 0.60 3:L:21::HG23 3:L:24::H 1.66 0.60 3:L:236:ILE:CG2 3:L:386:ILE:HD11 2.30 0.60 3:C:367:ILE:O 3:C:378::HA 2.01 0.60 1:G:58::HG12 1:G:59::N 2.16 0.60 2:H:172::HD21 3:I:113:ILE:HG22 1.78 0.60 3:I:209:ILE:H 3:I:209:ILE:HD12 1.66 0.60
Page 35 Full wwpdb X-ray Structure Validation Report 3GHG Atom-1 Atom-2 Interatomic Clash distance (Å) overlap (Å) 3:C:359::HG21 3:C:363:TYR:O 2.01 0.60 3:F:249::HB2 3:F:383::HG23 1.82 0.60 3:C:191:TRP:CH2 3:C:387:ILE:HG21 2.37 0.60 2:H:406::N 2:H:407:CYS:HA 2.16 0.60 7:K:471:NDG:C6 7:K:477:NDG:H8C2 2.11 0.60 3:L:153:CYS:HB2 3:L:192::OG1 2.02 0.60 1:A:139::O 1:A:142::HB3 2.00 0.60 2:B:75::HD13 1:D:44::O 2.00 0.60 1:J:207:MET:HE2 2:K:131::HE22 1.66 0.60 2:B:238::HG11 2:B:250::CG2 2.32 0.60 3:F:246::CD1 3:F:248::HG23 2.30 0.60 2:H:312:ILE:HG23 2:H:451::O 2.02 0.60 3:F:298::OD2 3:F:300::N 2.35 0.60 2:H:374::O 2:H:403:TRP:HA 2.02 0.60 2:K:412::HG3 2:K:450:MET:CE 2.31 0.60 3:I:387:ILE:O 3:I:387:ILE:HG23 2.02 0.60 2:K:169::HA 3:L:110::HD11 1.84 0.60 2:K:199::HG23 3:L:141::CA 2.31 0.60 2:K:139::HG21 3:L:79:ILE:HG21 1.84 0.60 2:E:126::O 2:E:130::N 2.31 0.60 1:J:132::HB3 3:L:107:ILE:HD11 1.83 0.60 3:C:293::CD1 3:C:370::HB1 2.37 0.59 7:E:477:NDG:H6C2 10:E:478:GAL:C1 2.32 0.59 3:I:79:ILE:O 3:I:83::N 2.25 0.59 2:B:179:ILE:CG2 2:B:180::N 2.64 0.59 2:E:253::HE21 2:E:253::C 2.06 0.59 2:E:405::O 2:E:406::CB 2.50 0.59 1:G:166::HB3 2:H:195::OG1 2.02 0.59 3:I:98::O 3:I:102::HG23 2.02 0.59 2:K:266:TRP:HA 2:K:377::HG21 1.84 0.59 3:L:349:TYR:OH 3:L:365::ND2 2.32 0.59 3:I:51::O 3:I:54::OG1 2.16 0.59 2:K:171:ILE:HG23 2:K:172::N 2.17 0.59 11:K:480:SIA:H7 11:K:480:SIA:O10 2.01 0.59 3:F:197::NH2 3:F:367:ILE:HD11 2.18 0.59 3:I:227:TRP:HE1 3:I:230::HD22 1.50 0.59 2:B:210::OE2 2:B:212::N 2.31 0.59 3:C:390::C 3:C:390::HD22 2.05 0.59 2:E:238::HG13 2:E:239:TYR:O 2.02 0.59 1:G:188::HG11 2:H:164::ND2 2.18 0.59 3:L:219::HG 3:L:224::HG22 1.67 0.59
Page 36 Full wwpdb X-ray Structure Validation Report 3GHG Atom-1 Atom-2 Interatomic Clash distance (Å) overlap (Å) 2:K:139::HG21 3:L:79:ILE:CG2 2.33 0.59 1:A:134::HA 1:A:137::OE1 2.03 0.59 2:E:146::O 2:E:150::N 2.25 0.59 2:H:333::OD1 2:H:335::HB3 2.03 0.59 1:A:185::O 1:A:185::HD22 2.01 0.59 2:E:432::OD1 2:E:443::OG 2.19 0.59 2:H:211:CYS:SG 2:H:250::HG23 2.43 0.59 3:I:11::HA 3:I:18:TYR:OH 2.02 0.59 2:B:257::OD1 2:B:257::N 2.35 0.59 3:C:227:TRP:HZ2 3:C:230::HD21 1.51 0.59 1:G:30::O 1:G:32::N 2.35 0.59 1:G:75::O 1:G:79::HB2 2.03 0.59 2:B:351::HD21 2:B:354:MET:H 1.50 0.59 3:C:126::O 3:C:129::HB3 2.03 0.59 1:D:55:ILE:HG23 2:E:86::CD1 2.32 0.59 1:J:127:ILE:O 1:J:130::HG12 2.03 0.59 2:B:434::O 2:B:436::N 2.36 0.58 3:C:246::HG 3:C:247::N 2.17 0.58 3:L:224::O 3:L:224::HG23 2.02 0.58 3:L:44::O 3:L:48::HB2 2.03 0.58 3:C:367:ILE:HG21 3:C:382::HG21 1.85 0.58 1:A:169::HD21 2:B:185::OD2 2.04 0.58 3:C:206::HB2 3:C:211:TYR:CE1 2.38 0.58 2:E:171:ILE:HG22 2:E:172::N 2.19 0.58 1:G:115::HD11 3:I:89:MET:CB 2.33 0.58 1:A:147:MET:SD 3:C:121:ILE:HD11 2.43 0.58 2:H:176::NH1 3:I:113:ILE:HG23 2.18 0.58 3:I:84::HD12 3:I:87::HD2 1.84 0.58 1:A:119:ILE:O 1:A:122::HB3 2.04 0.58 2:B:351::C 2:B:351::ND2 2.56 0.58 2:E:185::O 2:E:188::HB3 2.03 0.58 3:I:166::HD23 3:I:218::HB3 1.85 0.58 2:K:141::O 2:K:145::HB2 2.04 0.58 3:L:367:ILE:HG21 3:L:382::HG21 1.85 0.58 1:A:115::CD1 3:C:90::HB2 2.33 0.58 3:C:179::HD23 3:C:180::H 1.69 0.58 3:F:236:ILE:HG21 3:F:386:ILE:HD11 1.86 0.58 1:J:123::HA 1:J:126::HG12 1.85 0.58 1:J:207:MET:HA 1:J:210::HG12 1.86 0.58 3:F:393::HG23 3:F:394:ILE:HD12 1.85 0.58 1:J:73::HD13 1:J:73::C 2.24 0.58
Page 37 Full wwpdb X-ray Structure Validation Report 3GHG Atom-1 Atom-2 Interatomic Clash distance (Å) overlap (Å) 2:K:215:ILE:HD12 2:K:219::O 2.04 0.58 2:B:66::HD12 1:D:31::HB3 1.86 0.58 2:B:186::HG12 2:B:187::N 2.18 0.58 2:B:325::HB3 2:B:346::HG2 1.85 0.58 3:C:121:ILE:O 3:C:124::N 2.37 0.58 2:E:213::OE2 2:E:217::HE3 2.03 0.58 1:G:105::OD1 3:I:79:ILE:CD1 2.46 0.58 1:G:122::HB3 1:G:123::HZ2 1.69 0.58 2:K:144::HB3 2:K:148::HZ1 1.68 0.58 3:L:169:ILE:HD13 3:L:180::HG11 1.85 0.58 1:A:91:MET:O 1:A:95::N 2.37 0.57 2:B:142:TYR:O 2:B:146::HG 2.04 0.57 3:F:90::C 3:F:90::HD22 2.24 0.57 2:H:178::O 2:H:181::HG3 2.03 0.57 2:H:205::HG23 3:I:216::O 2.04 0.57 2:K:345:TYR:CB 2:K:354:MET:HE2 2.33 0.57 1:A:149::O 1:A:152::CG1 2.52 0.57 1:J:133:ILE:O 1:J:137::HG3 2.04 0.57 2:H:415::O 2:H:434::HA2 2.05 0.57 1:J:184::HE21 2:K:167::CG2 2.14 0.57 1:J:210::HG21 2:K:131::HG3 1.86 0.57 3:C:97::O 3:C:100:ILE:HG22 2.05 0.57 2:E:394:CYS:SG 2:E:406::HA 2.45 0.57 3:I:289::HA 3:I:371::HG23 1.87 0.57 2:B:205::O 2:B:205::CG1 2.53 0.57 1:D:122::HD12 1:D:123::HE3 1.86 0.57 3:F:197::CZ 3:F:367:ILE:HD11 2.35 0.57 1:G:150::O 1:G:154:ILE:HD13 2.04 0.57 2:H:251::HG22 2:H:453::HE2 1.86 0.57 2:E:312:ILE:HD11 2:E:452:MET:CE 2.35 0.57 1:G:108:TYR:CZ 3:I:82::HB1 2.38 0.57 1:J:58::HG22 1:J:62::CE1 2.39 0.57 1:A:70::HG2 2:B:100::HD21 1.86 0.57 2:B:179:ILE:HG23 2:B:180::H 1.70 0.57 2:E:210::OE1 2:E:213::N 2.30 0.57 2:E:310::HD12 2:E:311::N 2.19 0.57 3:F:189::HD22 3:F:391::HE 1.53 0.57 1:D:111::HG11 3:F:87::HB2 1.85 0.57 2:H:373:MET:HG3 2:H:405::HB2 1.85 0.57 1:J:136::O 1:J:140::HG13 2.05 0.57 2:K:140::OD1 2:K:140::N 2.38 0.57
Page 38 Full wwpdb X-ray Structure Validation Report 3GHG Atom-1 Atom-2 Interatomic Clash distance (Å) overlap (Å) 2:K:312:ILE:HD13 2:K:452:MET:HG2 1.86 0.57 2:K:333::ND2 2:K:335::HB3 2.20 0.57 2:B:311::HD12 2:B:312:ILE:N 2.20 0.57 1:D:94::HD13 2:E:125:TRP:CD1 2.40 0.57 3:F:250::HD23 3:F:379:MET:HE2 1.86 0.57 3:L:143::CG2 3:L:143::O 2.53 0.57 2:B:153:ILE:O 2:B:153:ILE:HG22 2.05 0.56 3:I:10:ILE:O 3:I:18:TYR:CZ 2.57 0.56 3:I:334:TRP:HB3 3:I:336:MET:HE1 1.87 0.56 9:K:473:MAN:C1 7:K:475:NDG:O 2.53 0.56 2:B:296::O 2:B:299:ILE:N 2.34 0.56 2:B:115::CE2 3:C:50::HG13 2.40 0.56 9:E:473:MAN:H62 10:E:476:GAL:H2 1.86 0.56 10:K:478:GAL:H5 11:K:479:SIA:O6 2.04 0.56 3:C:228::HD11 3:C:232::HD2 1.85 0.56 2:E:340:ILE:HG22 2:E:373:MET:O 2.05 0.56 3:L:228::HD11 3:L:232::HD2 1.87 0.56 9:B:473:MAN:C3 7:B:475:NDG:HA 2.17 0.56 3:F:217::C 3:F:218::HD23 2.26 0.56 3:I:338::N 3:I:339:CYS:HA 2.20 0.56 2:K:209::HA 2:K:228::O 2.04 0.56 1:A:169::H 2:B:189::NE2 2.04 0.56 3:C:246::HD21 3:C:248::HG22 1.88 0.56 1:D:94::HD22 2:E:125:TRP:NE1 2.20 0.56 3:L:259::O 3:L:286::HB3 2.06 0.56 11:E:479:SIA:H112 11:E:479:SIA:H7 1.88 0.56 2:H:224:MET:CE 2:H:237::HD3 2.36 0.56 2:H:351::HD21 2:H:354:MET:HG3 1.70 0.56 1:J:69::CD1 2:K:100::CD1 2.83 0.56 3:L:78:MET:O 3:L:81::N 2.38 0.56 1:A:122::HD13 1:A:122::C 2.26 0.56 1:A:70::HG3 2:B:100::HD11 1.87 0.56 1:D:169::HB2 2:E:189::HE22 1.70 0.56 2:E:345:TYR:CG 2:E:351::HB2 2.40 0.56 3:F:289::HA 3:F:371::HG23 1.87 0.56 1:G:58::HG13 1:G:62::CE2 2.40 0.56 3:I:209:ILE:HD12 3:I:209:ILE:N 2.21 0.56 2:K:101::OD1 3:L:43::HD13 2.06 0.56 3:F:249::C 3:F:250::HD12 2.26 0.56 1:J:162::HA 1:J:168::HB2 1.85 0.56 2:B:112::HA 2:B:115::CD2 2.41 0.56