Full wwpdb X-ray Structure Validation Report i
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- Ευρώπη Παπαδόπουλος
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1 Full wwpdb X-ray Structure Validation Report i Feb 15, :58 am GMT PDB ID : 3KLE Title : Crystal structure of AZT-resistant HIV-1 Reverse Transcriptase crosslinked to a DSDNA with a bound excision product, AZTPPPPA Authors : Tu, X.; Das, K.; Sarafianos, S.G.; Arnold, E. Deposited on : Resolution : 3.20 Å(reported) This is a Full wwpdb X-ray Structure Validation Report for a publicly released PDB entry. We welcome your comments at validation@mail.wwpdb.org A user guide is available at with specific help available everywhere you see the i symbol. The following versions of software and data (see references i ) were used in the production of this report: MolProbity : 4.02b-467 Mogul : (RC1), CSD as538be (2017) Xtriage (Phenix) : EDS : trunk28620 Percentile statistics : v01 (using entries in the PDB archive December 28th 2016) Refmac : CCP4 : Ideal geometry (proteins) : Engh & Huber (2001) Ideal geometry (DNA, RNA) : Parkinson et al. (1996) Validation Pipeline (wwpdb-vp) : recalc28949
2 Page 2 Full wwpdb X-ray Structure Validation Report 3KLE 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 3.20 Å. Percentile scores (ranging between 0-100) for global validation metrics of the entry are shown in the following graphic. The table shows the number of entries on which the scores are based. Metric Whole archive Similar resolution (#Entries) (#Entries, resolution range(å)) R free ( ) Clashscore ( ) Ramachandran outliers ( ) Sidechain outliers ( ) RSRZ outliers ( ) 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 E I M B F 437
3 Page 3 Full wwpdb X-ray Structure Validation Report 3KLE Mol Chain Length Quality of chain 2 J N C 27 3 G 27 3 K 27 3 O 27 4 D 21 4 H 21 4 L 21 4 P 21 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 7 GOL B X
4 Page 4 Full wwpdb X-ray Structure Validation Report 3KLE 2 Entry composition i There are 9 unique types of molecules in this entry. The entry contains atoms, of which 0 are hydrogens and 0 are deuteriums. In the tables below, the ZeroOcc column contains the number of atoms modelled with zero occupancy, the AltConf column contains the number of residues with at least one atom in alternate conformation and the Trace column contains the number of residues modelled with at most 2 atoms. Molecule 1 is a protein called Reverse transcriptase/ribonuclease H. Mol Chain Residues Atoms ZeroOcc AltConf Trace 1 A 560 Total C N O S E 560 Total C N O S I 560 Total C N O S M 560 Total C N O S There are 40 discrepancies between the modelled and reference sequences: Chain Residue Modelled Actual Comment Reference A -1 MET - EXPRESSION TAG UNP P03366 A 0 VAL - EXPRESSION TAG UNP P03366 A 41 LEU MET ENGINEERED UNP P03366 A 67 ASN ASP ENGINEERED UNP P03366 A 70 ARG LYS ENGINEERED UNP P03366 A 215 TYR THR ENGINEERED UNP P03366 A 219 GLN LYS ENGINEERED UNP P03366 A 258 CYS GLN ENGINEERED UNP P03366 A 280 SER CYS ENGINEERED UNP P03366 A 559 VAL ILE SEE REMERK 999 UNP P03366 E -1 MET - EXPRESSION TAG UNP P03366 E 0 VAL - EXPRESSION TAG UNP P03366 E 41 LEU MET ENGINEERED UNP P03366 E 67 ASN ASP ENGINEERED UNP P03366 E 70 ARG LYS ENGINEERED UNP P03366 E 215 TYR THR ENGINEERED UNP P03366 E 219 GLN LYS ENGINEERED UNP P03366 E 258 CYS GLN ENGINEERED UNP P03366 E 280 SER CYS ENGINEERED UNP P03366 E 559 VAL ILE SEE REMERK 999 UNP P03366 I -1 MET - EXPRESSION TAG UNP P03366
5 Page 5 Full wwpdb X-ray Structure Validation Report 3KLE Chain Residue Modelled Actual Comment Reference I 0 VAL - EXPRESSION TAG UNP P03366 I 41 LEU MET ENGINEERED UNP P03366 I 67 ASN ASP ENGINEERED UNP P03366 I 70 ARG LYS ENGINEERED UNP P03366 I 215 TYR THR ENGINEERED UNP P03366 I 219 GLN LYS ENGINEERED UNP P03366 I 258 CYS GLN ENGINEERED UNP P03366 I 280 SER CYS ENGINEERED UNP P03366 I 559 VAL ILE SEE REMERK 999 UNP P03366 M -1 MET - EXPRESSION TAG UNP P03366 M 0 VAL - EXPRESSION TAG UNP P03366 M 41 LEU MET ENGINEERED UNP P03366 M 67 ASN ASP ENGINEERED UNP P03366 M 70 ARG LYS ENGINEERED UNP P03366 M 215 TYR THR ENGINEERED UNP P03366 M 219 GLN LYS ENGINEERED UNP P03366 M 258 CYS GLN ENGINEERED UNP P03366 M 280 SER CYS ENGINEERED UNP P03366 M 559 VAL ILE SEE REMERK 999 UNP P03366 Molecule 2 is a protein called p51 RT. Mol Chain Residues Atoms ZeroOcc AltConf Trace 2 B 425 Total C N O S F 419 Total C N O S J 419 Total C N O S N 419 Total C N O S There are 40 discrepancies between the modelled and reference sequences: Chain Residue Modelled Actual Comment Reference B 280 SER CYS ENGINEERED UNP P03366 B 429 GLY - EXPRESSION TAG UNP P03366 B 430 GLY - EXPRESSION TAG UNP P03366 B 431 HIS - EXPRESSION TAG UNP P03366 B 432 HIS - EXPRESSION TAG UNP P03366 B 433 HIS - EXPRESSION TAG UNP P03366 B 434 HIS - EXPRESSION TAG UNP P03366
6 Page 6 Full wwpdb X-ray Structure Validation Report 3KLE Chain Residue Modelled Actual Comment Reference B 435 HIS - EXPRESSION TAG UNP P03366 B 436 HIS - EXPRESSION TAG UNP P03366 B 437 HIS - EXPRESSION TAG UNP P03366 F 280 SER CYS ENGINEERED UNP P03366 F 429 GLY - EXPRESSION TAG UNP P03366 F 430 GLY - EXPRESSION TAG UNP P03366 F 431 HIS - EXPRESSION TAG UNP P03366 F 432 HIS - EXPRESSION TAG UNP P03366 F 433 HIS - EXPRESSION TAG UNP P03366 F 434 HIS - EXPRESSION TAG UNP P03366 F 435 HIS - EXPRESSION TAG UNP P03366 F 436 HIS - EXPRESSION TAG UNP P03366 F 437 HIS - EXPRESSION TAG UNP P03366 J 280 SER CYS ENGINEERED UNP P03366 J 429 GLY - EXPRESSION TAG UNP P03366 J 430 GLY - EXPRESSION TAG UNP P03366 J 431 HIS - EXPRESSION TAG UNP P03366 J 432 HIS - EXPRESSION TAG UNP P03366 J 433 HIS - EXPRESSION TAG UNP P03366 J 434 HIS - EXPRESSION TAG UNP P03366 J 435 HIS - EXPRESSION TAG UNP P03366 J 436 HIS - EXPRESSION TAG UNP P03366 J 437 HIS - EXPRESSION TAG UNP P03366 N 280 SER CYS ENGINEERED UNP P03366 N 429 GLY - EXPRESSION TAG UNP P03366 N 430 GLY - EXPRESSION TAG UNP P03366 N 431 HIS - EXPRESSION TAG UNP P03366 N 432 HIS - EXPRESSION TAG UNP P03366 N 433 HIS - EXPRESSION TAG UNP P03366 N 434 HIS - EXPRESSION TAG UNP P03366 N 435 HIS - EXPRESSION TAG UNP P03366 N 436 HIS - EXPRESSION TAG UNP P03366 N 437 HIS - EXPRESSION TAG UNP P03366 Molecule 3 is a DNA chain called DNA (25-MER). Mol Chain Residues Atoms ZeroOcc AltConf Trace 3 C 25 Total C N O P G 25 Total C N O P K 25 Total C N O P
7 Page 7 Full wwpdb X-ray Structure Validation Report 3KLE Mol Chain Residues Atoms ZeroOcc AltConf Trace 3 O 25 Total C N O P Molecule 4 is a DNA chain called DNA (5 -D(*AP*CP*AP*GP*TP*CP*CP*CP*TP*GP* TP*TP*CP*GP*GP*(MRG)P*CP*GP*CP*CP*(2DA))-3 ). Mol Chain Residues Atoms ZeroOcc AltConf Trace 4 D 21 Total C N O P S H 21 Total C N O P S L 21 Total C N O P S P 21 Total C N O P S Molecule 5 is MAGNESIUM ION (three-letter code: MG) (formula: Mg). Mol Chain Residues Atoms ZeroOcc AltConf Total Mg 5 I Total Mg 5 A Total Mg 5 M Total Mg 5 E Molecule 6 is [[[[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2 -YL]METHOXY-HYDROXY-PHOSPHORYL]OXY-HYDROXY-PHOSPHORYL]OXY-H YDROXY-PHOSPHORYL] [(2S,3S,5R)-3-AZIDO-5-(5-METHYL-2,4-DIOXO-PYRIMID IN-1-YL)OXOLAN-2-YL]METHYL HYDROGEN PHOSPHATE (three-letter code: ZP4) (formula: C 20 H 28 N 10 O 19 P 4 ).
8 Page 8 Full wwpdb X-ray Structure Validation Report 3KLE Mol Chain Residues Atoms ZeroOcc AltConf 6 A 1 Total C N O P E 1 Total C N O P I 1 Total C N O P M 1 Total C N O P Molecule 7 is GLYCEROL (three-letter code: GOL) (formula: C 3 H 8 O 3 ).
9 Page 9 Full wwpdb X-ray Structure Validation Report 3KLE Mol Chain Residues Atoms ZeroOcc AltConf 7 B 1 Total C O F 1 Total C O Molecule 8 is ALPHA-D-FRUCTOFURANOSYL ALPHA-D-GLUCOPYRANOSIDE (three-letter code: SWE) (formula: C 12 H 22 O 11 ). Mol Chain Residues Atoms ZeroOcc AltConf 8 J 1 Total C O Molecule 9 is water. Mol Chain Residues Atoms ZeroOcc AltConf Total O 9 A Total O 9 B Total O 9 E Total O 9 F Total O 9 I J Total O 14 14
10 Page 10 Full wwpdb X-ray Structure Validation Report 3KLE Mol Chain Residues Atoms ZeroOcc AltConf Total O 9 M Total O 9 N Total O 9 C Total O 9 D Total O 9 G Total O 9 H Total O 9 K Total O 9 L Total O 9 O Total O 9 P
11 Page 11 Full wwpdb X-ray Structure Validation Report 3KLE 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 and 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: Reverse transcriptase/ribonuclease H Chain A: I506 Q507 A508 Q509 P510 D511 K512 S513 L517 V518 N519 Q520 I521 I522 E523 Q524 L525 K528 V531 Y532 L533 A534 W535 I542 G543 G544 N545 E546 Q547 V548 D549 K550 L551 V552 I556 R557 K558 V559 L560 V435 G436 A437 E438 T439 F440 Y441 V442 N447 R448 E449 T450 K451 L452 G453 K454 A455 G456 Y457 V458 K461 G462 R463 Q464 K465 V466 V467 P468 L469 T470 N471 T472 T473 K476 T477 E478 L479 Q480 A481 I482 A485 L486 S489 E492 V493 N494 I495 V496 S499 Q500 Y501 A502 L503 R356 M357 H361 T362 N363 D364 V365 K366 Q367 E370 I375 I382 K385 T386 P387 K388 F389 K390 Q394 T397 W398 E399 T400 W401 W402 W406 Q407 A408 T409 W410 I411 P412 E413 F416 V417 N418 T419 P420 P421 L422 L425 W426 Y427 Q428 L429 E430 K431 E432 P433 I434 G285 A288 L289 T290 E291 V292 I293 P294 L295 T296 E297 E298 A299 E300 L301 E302 L303 A304 E305 N306 R307 E308 I309 H315 G316 V317 D320 K323 D324 L325 I326 I329 Q330 K331 Q332 Q336 W337 T338 Y339 Q340 I341 Y342 Q343 E344 K347 N348 L349 K350 T351 G352 K353 Y354 A355 T216 P217 D218 Q219 K220 H221 Q222 K223 E224 P225 P226 F227 L228 W229 M230 G231 Y232 E233 L234 H235 P236 D237 K238 Q242 P243 I244 V245 L246 D250 S251 W252 T253 V254 N255 K259 L260 K263 L264 N265 W266 Q269 I270 Y271 P272 G273 I274 R277 Q278 L279 S280 K281 L282 L283 R284 G152 W153 K154 G155 S156 P157 A158 I159 F160 Q161 S162 S163 M164 T165 K166 I167 L168 E169 P170 F171 K172 K173 Q174 N175 P176 D177 I178 V179 I180 Y181 Q182 Y183 M184 L187 Y188 S191 E194 I195 G196 Q197 H198 R199 T200 K201 I202 E203 E204 L205 R206 Q207 H208 L209 L210 R211 L214 Y215 F77 N81 K82 R83 T84 Q85 D86 E89 V90 Q91 I94 P95 H96 P97 A98 G99 L100 K101 K102 K103 V106 T107 V108 L109 D113 A114 Y115 F116 S117 V118 P119 L120 D121 E122 F130 T131 I132 I135 N136 N137 E138 G141 I142 R143 Y144 Q145 Y146 N147 V148 L149 P150 Q151 MET VAL P1 I2 S3 P4 I5 V8 P9 V10 G15 M16 D17 G18 P19 K20 V21 K22 Q23 W24 P25 L26 T27 E28 E29 K30 I31 K32 A33 L34 V35 E36 K46 K49 P52 E53 N54 P55 T58 P59 V60 K64 N67 S68 T69 R70 W71 R72 K73 L74 V75 D76 Molecule 1: Reverse transcriptase/ribonuclease H Chain E: K73 L74 V75 D76 F77 R78 E79 R83 T84 Q85 D86 V90 Q91 H96 P97 A98 K102 K103 V108 L109 D110 V111 G112 D113 A114 Y115 F116 S117 V118 P119 L120 D121 E122 F130 T131 I132 P133 S134 I135 N136 N137 E138 G141 I142 R143 Y144 Q145 Y146 N147 V148 L149 P150 Q151 MET VAL P1 I2 S3 P4 I5 P9 V10 K11 L12 K13 D17 G18 K22 Q23 W24 P25 L26 T27 E28 E29 K30 I31 K32 A33 L34 V35 E36 I37 E40 E44 G45 K46 K49 I50 G51 P52 E53 N54 P55 Y56 V60 K64 K65 K66 N67 S68 T69 R70 W71 R72
12 Page 12 Full wwpdb X-ray Structure Validation Report 3KLE K512 S513 E514 S515 E516 L517 V518 N519 Q520 I521 I522 E523 Q524 K528 E529 K530 V531 Y532 L533 A534 W535 G543 G544 Q547 V548 D549 K550 L551 V552 S553 A554 G555 I556 R557 K558 V559 L560 E438 T439 F440 Y441 V442 A446 N447 R448 E449 T450 K451 L452 V458 K461 G462 R463 Q464 K465 V466 V467 P468 L469 T470 N471 T472 T473 K476 T477 E478 L479 Q480 A481 I482 A485 L486 S489 E492 V493 N494 I495 V496 S499 Q500 L503 I506 Q507 A508 Q509 P510 D511 T362 N363 D364 V365 K366 Q367 L368 T369 E370 I375 I382 K385 T386 P387 K388 F389 K390 Q394 K395 E396 T397 W398 E399 T400 W401 W402 W406 Q407 A408 T409 W410 I411 P412 E413 W414 E415 F416 V417 N418 T419 P420 P421 L422 L425 W426 Y427 Q428 L429 E432 P433 I434 V435 L295 T296 E297 E298 A299 E300 L301 E302 L303 A304 E305 N306 R307 E308 I309 H315 G316 V317 Y318 Y319 D320 K323 D324 L325 I326 A327 E328 I329 Q330 K331 Q332 Q336 W337 T338 Y339 Q340 I341 Y342 Q343 E344 P345 F346 K347 N348 L349 K350 T351 G352 K353 Y354 A355 R356 M357 R358 G359 A360 H361 K223 E224 P225 P226 F227 L228 W229 M230 G231 Y232 E233 L234 H235 P236 D237 K238 Q242 P243 I244 D250 S251 W252 T253 V254 N255 D256 I257 C258 K259 L260 V261 G262 K263 L264 Q269 I274 K275 V276 R277 Q278 L279 S280 K281 L282 L283 R284 G285 T286 K287 A288 L289 T290 E291 V292 I293 P294 G152 W153 K154 P157 A158 Q161 S162 S163 M164 T165 K166 I167 L168 E169 P170 F171 K172 K173 Q174 N175 P176 V179 I180 Y181 Q182 Y183 M184 D185 D186 L187 Y188 E194 I195 R199 T200 K201 E204 L205 R206 Q207 H208 L209 L210 R211 W212 G213 L214 Y215 T216 Q219 K220 H221 Q222 Molecule 1: Reverse transcriptase/ribonuclease H Chain I: L479 Q480 A481 A485 L486 S489 G490 L491 E492 V493 N494 I495 V496 S499 Q500 L503 Q507 A508 Q509 P510 D511 K512 S515 E516 L517 V518 I521 I522 E523 Q524 L525 K528 E529 K530 V531 Y532 L533 A534 W535 G543 G544 Q547 V548 D549 K550 L551 V552 S553 I556 W410 I411 P412 E413 F416 V417 N418 T419 P420 P421 L422 L425 W426 Y427 Q428 E432 P433 I434 V435 G436 A437 E438 T439 F440 Y441 V442 N447 R448 E449 T450 K451 L452 G453 K454 A455 G456 Y457 V458 T459 N460 K461 G462 R463 Q464 K465 V466 L469 T470 N471 T472 T473 K476 T477 E478 Q332 Q336 W337 T338 Y339 Q340 I341 Y342 Q343 E344 P345 F346 K347 N348 L349 K350 T351 Y354 A355 R356 H361 T362 N363 D364 V365 K366 Q367 L368 T369 E370 K374 I375 I382 W383 G384 K385 T386 P387 K388 F389 K390 Q394 T397 W398 E399 T400 W401 W402 W406 Q407 A408 T409 I270 Y271 P272 G273 I274 K275 V276 R277 Q278 L279 S280 K281 L282 L283 R284 G285 T286 K287 A288 L289 T290 E291 V292 I293 P294 L295 T296 E297 E298 A299 E300 L301 E302 L303 A304 E305 N306 R307 E308 I309 E312 H315 G316 V317 Y318 Y319 D320 P321 S322 K323 D324 L325 I326 A327 E328 I329 Q330 K331 T200 E203 E204 L205 R206 Q207 H208 L209 L210 R211 W212 G213 L214 D218 Q219 K220 H221 Q222 K223 E224 P225 P226 F227 L228 W229 M230 G231 Y232 E233 L234 H235 P236 D237 K238 W239 Q242 P243 I244 V245 L246 P247 E248 K249 D250 S251 W252 T253 V254 N255 K259 L260 K263 L264 Q269 P133 S134 I135 N136 N137 E138 G141 I142 R143 Y144 Q145 Y146 N147 V148 L149 P150 Q151 G152 W153 K154 G155 S156 P157 A158 I159 F160 Q161 S162 S163 M164 I167 L168 E169 P170 F171 K172 K173 Q174 N175 P176 D177 I178 V179 I180 Y181 L187 Y188 S191 D192 L193 E194 I195 G196 Q197 H198 R199 K65 K66 N67 S68 T69 R70 W71 R72 K73 L74 V75 D76 F77 R78 E79 L80 N81 K82 R83 T84 Q85 D86 V90 Q91 I94 P95 A98 G99 L100 K101 K102 K103 K104 S105 V106 T107 V108 L109 D113 A114 Y115 F116 S117 V118 P119 L120 D121 E122 D123 F124 T128 A129 F130 T131 I132 MET VAL P1 I2 S3 P4 I5 E6 T7 V8 P9 V10 K11 L12 K13 P14 D17 G18 P19 K20 V21 K22 Q23 W24 P25 L26 T27 K30 I31 K32 A33 L34 V35 C38 T39 E40 E44 G45 K46 I47 S48 K49 I50 G51 P52 E53 N54 P55 Y56 N57 T58 P59 V60 I63 K64
13 Page 13 Full wwpdb X-ray Structure Validation Report 3KLE R557 K558 V559 L560 Molecule 1: Reverse transcriptase/ribonuclease H Chain M: L517 V518 N519 Q520 I521 I522 E523 Q524 K528 E529 K530 V531 Y532 L533 A534 W535 I542 G543 G544 N545 E546 Q547 V548 D549 K550 L551 V552 S553 A554 G555 I556 R557 K558 V559 L560 R448 E449 T450 K451 L452 G453 K454 A455 G456 Y457 V458 T459 N460 K461 G462 R463 Q464 K465 V466 L469 T470 N471 T472 T473 K476 T477 E478 L479 Q480 A481 I482 A485 S489 E492 V493 N494 I495 V496 S499 Q500 Y501 A502 L503 G504 I505 I506 Q507 A508 Q509 P510 D511 K512 S513 T376 T377 I382 W383 G384 K385 T386 P387 K388 F389 K390 L391 P392 I393 Q394 K395 E396 T397 W398 E399 T400 W401 W402 W406 Q407 A408 T409 W410 I411 P412 E413 W414 E415 F416 V417 N418 T419 P420 P421 L422 V423 K424 L425 W426 Y427 E432 P433 I434 V435 G436 A437 E438 T439 V442 N447 L310 P313 V314 H315 G316 V317 Y318 Y319 D320 K323 D324 L325 I326 A327 E328 I329 Q330 K331 Q332 G335 Q336 W337 T338 Y339 Q340 I341 Y342 Q343 E344 P345 F346 K347 N348 L349 K350 T351 G352 K353 Y354 A355 R356 M357 H361 T362 N363 D364 V365 K366 Q367 L368 T369 E370 A371 K374 I375 L246 P247 E248 K249 D250 S251 W252 T253 V254 N255 C258 K259 L260 V261 G262 K263 L264 Q269 I270 Y271 P272 G273 I274 K275 V276 R277 Q278 L279 S280 K281 L282 L283 R284 G285 T286 K287 A288 L289 T290 E291 V292 I293 P294 L295 T296 E297 E298 A299 E300 L301 E302 L303 A304 E305 N306 R307 E308 I309 Y183 M184 D185 D186 L187 Y188 V189 D192 L193 E194 I195 G196 Q197 H198 R199 T200 E203 E204 L205 R206 Q207 H208 L209 L210 R211 W212 G213 L214 Y215 T216 P217 D218 Q219 K220 H221 Q222 K223 E224 P225 P226 F227 L228 W229 M230 G231 Y232 E233 L234 H235 P236 D237 K238 V241 Q242 P243 I244 V245 D121 E122 D123 F124 Y127 T128 A129 F130 T131 I132 P133 S134 I135 N136 N137 E138 G141 I142 R143 Y144 Q145 Y146 N147 V148 L149 P150 Q151 G152 W153 K154 G155 S156 P157 A158 I159 F160 Q161 S162 S163 M164 T165 K166 I167 L168 E169 P170 F171 K172 K173 Q174 N175 P176 D177 I178 V179 I180 Y181 Q182 V60 I63 K64 K65 K66 N67 S68 T69 R70 W71 R72 K73 L74 V75 D76 F77 R78 E79 L80 N81 K82 R83 T84 Q85 D86 F87 W88 E89 V90 Q91 L92 G93 I94 P95 H96 P97 A98 G99 L100 K101 K102 K103 K104 S105 V106 T107 V108 L109 D110 V111 G112 D113 A114 Y115 F116 S117 V118 P119 L120 MET VAL P1 I2 S3 P4 I5 E6 T7 V8 P9 V10 K11 L12 K13 P14 G15 M16 D17 G18 P19 K20 V21 K22 Q23 W24 P25 L26 T27 E28 E29 K30 I31 K32 A33 L34 V35 E36 I37 C38 T39 E40 L41 E42 K43 E44 G45 K46 I47 S48 K49 I50 G51 P52 E53 N54 P55 Y56 N57 Molecule 2: p51 RT Chain B: K154 G155 S156 P157 F160 Q161 S162 S163 M164 E169 P170 F171 Q174 N175 P176 Y181 Q182 Y183 M184 L187 Y188 V189 G190 L193 E194 I195 G196 R199 T200 K201 I202 E203 R206 Q207 H208 L209 L210 R211 Q222 LYS GLU PRO PRO PHE LEU TRP MET G231 Y232 E233 L234 E79 L80 N81 K82 R83 T84 Q85 W88 I94 P95 H96 L100 K101 K102 S105 V108 L109 D110 V111 Y115 F116 S117 V118 P119 L120 D121 E122 D123 F124 R125 F130 T131 I132 P133 N136 N137 E138 T139 P140 G141 I142 R143 Y144 Q145 Y146 N147 V148 L149 P150 Q151 G152 W153 PRO ILE S3 E6 T7 K13 M16 D17 K20 V21 W24 P25 L26 T27 E28 E29 K30 I31 K32 A33 L34 V35 E36 I37 C38 T39 E40 M41 E42 K43 K46 I50 N54 P59 V60 F61 A62 I63 K64 D67 S68 T69 R72 K73 L74 V75 D76 F77 R78
14 Page 14 Full wwpdb X-ray Structure Validation Report 3KLE L391 P392 I393 Q394 K395 E396 T397 W398 E399 T400 W401 W402 T403 T409 W410 E413 N418 T419 P420 P421 L422 V423 K424 L425 W426 Y427 Q428 G429 G430 H431 H432 H433 H434 H435 HIS HIS G316 V317 Y318 Y319 L325 E328 I329 Q330 G333 Q334 G335 Q336 W337 T338 Y339 E344 K350 T351 G352 K353 Y354 A355 R356 M357 R358 G359 A360 N363 D364 V365 K366 Q367 L368 T369 E370 A371 V372 Q373 K374 I375 T376 T377 E378 S379 I380 W383 G384 K385 T386 P387 K388 F389 K390 H235 P236 D237 K238 W239 T240 V241 Q242 P243 I244 V245 L246 P247 E248 W252 T253 V254 N255 D256 I257 Q258 K259 L260 V261 G262 K263 L264 N265 W266 I270 Y271 I274 K275 V276 K281 L282 L283 R284 G285 T286 L289 T290 L295 L303 A304 E305 N306 R307 L310 V314 H315 Molecule 2: p51 RT Chain F: A371 V372 Q373 K374 I375 T376 T377 E378 S379 I380 V381 I382 W383 G384 K385 T386 P387 K388 F389 K390 I393 Q394 K395 E396 T397 W398 E399 T400 W401 W402 T403 T409 W410 E413 W414 E415 N418 T419 P420 P421 L422 V423 K424 L425 W426 G429 GLY HIS HIS HIS HIS HIS HIS HIS G285 T286 L289 T290 L295 L303 A304 E305 N306 R307 L310 V314 H315 G316 V317 Y318 Y319 L325 E328 I329 Q330 G333 Q334 G335 Q336 W337 T338 Y339 E344 L349 K350 T351 G352 K353 Y354 A355 R356 M357 R358 G359 A360 H361 D364 V365 K366 Q367 L368 T369 E370 G213 T216 P217 D218 K219 Q222 LYS GLU PRO PRO PHE LEU TRP MET G231 Y232 E233 L234 H235 P236 D237 K238 W239 T240 V241 Q242 P243 I244 V245 L246 P247 E248 W252 T253 V254 I257 V261 L264 N265 W266 A267 S268 Q269 I270 Y271 I274 K275 V276 K281 L282 L283 R284 R143 Y144 Q145 Y146 N147 V148 L149 P150 Q151 G152 W153 K154 G155 S156 P157 A158 I159 F160 Q161 S162 S163 M164 T165 E169 P170 F171 Q174 N175 P176 Y181 Q182 Y183 M184 L187 Y188 V189 G190 L193 E194 I195 G196 R199 T200 K201 I202 E203 R206 Q207 H208 L209 L210 R211 W212 R72 K73 L74 V75 D76 F77 R78 E79 L80 N81 K82 R83 T84 Q85 D86 F87 W88 E89 I94 P95 H96 L100 K101 K104 S105 V106 T107 V108 L109 D110 V111 Y115 F116 S117 V118 P119 L120 D121 E122 D123 F124 R125 F130 T131 I132 P133 S134 I135 N136 N137 E138 T139 P140 G141 I142 PRO ILE S3 P4 I5 E6 T7 V8 P9 V10 K13 M16 D17 K20 V21 K22 Q23 W24 P25 L26 T27 E28 E29 K30 I31 K32 A33 L34 V35 E36 I37 C38 T39 E40 M41 E42 K43 E44 G45 K46 I47 S48 K49 I50 P59 V60 F61 A62 I63 K64 K65 K66 D67 S68 T69 Molecule 2: p51 RT Chain J: K201 I202 E203 E204 L205 R206 Q207 H208 L209 L210 R211 L214 T215 T216 P217 D218 K219 K220 H221 Q222 LYS GLU PRO PRO PHE LEU TRP MET G231 Y232 E233 L234 H235 P236 D237 K238 W239 T240 V241 Q242 P243 I244 V245 L246 P247 E248 K249 D250 S251 W252 T253 V254 N255 D256 I257 Q258 K259 L260 V261 N137 E138 T139 P140 G141 I142 R143 Y144 Q145 Y146 N147 V148 L149 P150 Q151 G152 W153 K154 G155 S156 P157 A158 I159 F160 Q161 S162 S163 M164 T165 K166 I167 L168 E169 P170 F171 Q174 N175 P176 D177 I178 V179 I180 Y181 Q182 Y183 M184 L187 Y188 V189 D192 L193 E194 I195 G196 R199 T200 R72 K73 L74 V75 D76 F77 R78 E79 L80 N81 K82 R83 T84 Q85 D86 F87 W88 L92 G93 I94 P95 H96 P97 L100 K101 K102 K103 K104 S105 V106 T107 V108 L109 D110 V111 G112 D113 A114 Y115 V118 P119 L120 D121 E122 D123 F124 R125 K126 Y127 F130 T131 I132 P133 S134 I135 N136 PRO ILE S3 P4 I5 E6 T7 V8 P9 V10 K11 L12 K13 M16 D17 K20 V21 W24 P25 L26 T27 E28 E29 K30 I31 K32 A33 L34 V35 E36 I37 M41 E42 I47 I50 E53 N54 N57 T58 P59 V60 F61 A62 I63 K64 K65 K66 D67 S68 T69 K70 W71
15 Page 15 Full wwpdb X-ray Structure Validation Report 3KLE N418 T419 P420 P421 L422 V423 K424 L425 W426 Y427 Q428 G429 GLY HIS HIS HIS HIS HIS HIS HIS K350 T351 G352 K353 Y354 A355 R356 M357 R358 G359 A360 H361 D364 V365 K366 Q367 L368 T369 E370 A371 V372 Q373 K374 I375 T376 T377 E378 S379 I380 V381 I382 W383 G384 K385 T386 P387 K388 F389 K390 L391 P392 I393 Q394 K395 E396 T397 W398 E399 T400 W401 W402 T403 Q407 A408 T409 W410 E413 G262 K263 L264 N265 W266 A267 S268 Q269 I270 Y271 I274 K275 V276 K281 L282 L283 R284 G285 T286 K287 A288 L289 T290 L303 R307 V314 H315 G316 V317 Y318 Y319 D320 P321 L325 I326 A327 E328 I329 Q330 G333 Q334 G335 Q336 W337 T338 Y339 Q340 I341 Y342 Q343 E344 L349 Molecule 2: p51 RT Chain N: P387 K388 F389 K390 L391 P392 I393 Q394 K395 E396 T397 W398 E399 T400 W401 W402 T403 A408 T409 W410 I411 P412 E413 W414 E415 F416 V417 N418 T419 P420 P421 L422 V423 K424 L425 W426 Y427 Q428 G429 GLY HIS HIS HIS HIS HIS HIS HIS I326 A327 E328 I329 Q330 G333 Q334 G335 Q336 W337 T338 Y339 Q340 I341 Y342 Q343 E344 P345 F346 K347 N348 L349 K350 T351 G352 K353 Y354 A355 R356 M357 R358 G359 A360 H361 T362 N363 D364 V365 K366 Q367 L368 T369 E370 A371 V372 Q373 K374 I375 T376 T377 E378 S379 I380 V381 I382 W383 G384 K385 T386 W252 T253 V254 I257 Q258 K259 L260 V261 G262 K263 L264 N265 W266 A267 S268 Q269 I270 Y271 I274 K275 V276 R277 Q278 K281 L282 L283 R284 G285 T286 K287 A288 L289 T290 E291 V292 I293 E298 L303 N306 R307 V314 H315 G316 V317 Y318 Y319 D320 P321 S322 K323 D324 L325 V189 G190 S191 D192 L193 E194 I195 G196 Q197 H198 R199 T200 K201 I202 E203 E204 L205 R206 Q207 H208 L209 L210 R211 W212 G213 L214 T215 T216 P217 D218 K219 K220 H221 Q222 LYS GLU PRO PRO PHE LEU TRP MET G231 Y232 E233 L234 H235 P236 D237 K238 W239 T240 V241 Q242 P243 I244 V245 L246 P247 E248 Y127 T128 A129 F130 T131 I132 P133 S134 I135 N136 N137 E138 T139 P140 G141 I142 R143 Y144 Q145 Y146 N147 V148 L149 P150 Q151 G152 W153 K154 G155 S156 P157 A158 I159 F160 Q161 S162 S163 M164 T165 K166 I167 L168 E169 P170 F171 Q174 N175 P176 D177 I178 V179 I180 Y181 Q182 Y183 M184 L187 Y188 K66 D67 S68 T69 K70 W71 R72 K73 L74 V75 D76 F77 R78 E79 L80 N81 K82 R83 T84 Q85 D86 F87 W88 E89 V90 Q91 L92 G93 I94 P95 H96 P97 A98 G99 L100 K101 K102 K103 K104 S105 V106 T107 V108 L109 D110 V111 A114 Y115 F116 S117 V118 P119 L120 D121 E122 D123 F124 R125 K126 PRO ILE S3 P4 I5 E6 T7 V8 P9 V10 K11 L12 K13 M16 D17 G18 P19 K20 V21 K22 Q23 W24 P25 L26 T27 E28 E29 K30 I31 K32 A33 L34 V35 E36 I37 C38 T39 E40 M41 K46 I47 I50 G51 P52 E53 N54 P55 Y56 N57 T58 P59 V60 F61 A62 I63 K64 K65 Molecule 3: DNA (25-MER) Chain C: DA DT G703 C704 A705 T706 G707 G708 C709 G710 C711 C712 C713 G714 C717 A718 C723 T724 G725 T726 G727 Molecule 3: DNA (25-MER) Chain G: DA DT G703 C704 A705 T706 G707 G708 C709 G710 C711 C712 C713 G714 C717 A718 C723 T724 G725 T726 G727
16 Page 16 Full wwpdb X-ray Structure Validation Report 3KLE Molecule 3: DNA (25-MER) Chain K: DA DT G703 C704 A705 T706 G707 G708 C709 G710 C711 C712 C713 G714 A715 A716 C717 A718 C723 T724 G725 T726 G727 Molecule 3: DNA (25-MER) Chain O: DA DT G703 C704 A705 T706 G707 G708 C709 G710 C711 C712 C713 G714 A715 A716 C717 A718 C723 T724 G725 T726 G727 Molecule 4: DNA (5 -D(*AP*CP*AP*GP*TP*CP*CP*CP*TP*GP*TP*TP*CP*GP*GP*(M RG)P*CP*GP*CP*CP*(2DA))-3 ) Chain D: A802 C803 A804 G805 T806 G815 G816 G817 C818 G819 C820 C821 A822 Molecule 4: DNA (5 -D(*AP*CP*AP*GP*TP*CP*CP*CP*TP*GP*TP*TP*CP*GP*GP*(M RG)P*CP*GP*CP*CP*(2DA))-3 ) Chain H: A802 C803 G815 G816 G817 C818 G819 C820 C821 A822 Molecule 4: DNA (5 -D(*AP*CP*AP*GP*TP*CP*CP*CP*TP*GP*TP*TP*CP*GP*GP*(M RG)P*CP*GP*CP*CP*(2DA))-3 ) Chain L: A802 C803 A804 G805 T806 C809 G815 G816 G817 C818 G819 C820 C821 A822 Molecule 4: DNA (5 -D(*AP*CP*AP*GP*TP*CP*CP*CP*TP*GP*TP*TP*CP*GP*GP*(M RG)P*CP*GP*CP*CP*(2DA))-3 ) Chain P: A802 C803 A804 G805 T806 C809 C814 G815 G816 G817 C818 G819 C820 C821 A822
17 Page 17 Full wwpdb X-ray Structure Validation Report 3KLE 4 Data and refinement statistics i Property Value Source Space group P Depositor Cell constants 78.74Å Å Å a, b, c, α, β, γ Depositor Resolution (Å) Depositor EDS % Data completeness (in resolution range) 90.4 ( ) 88.8 ( ) Depositor EDS R merge 0.12 Depositor R sym (Not available) Depositor < I/σ(I) > (at 3.17Å) Xtriage Refinement program CNS 1.2 Depositor 0.280, Depositor R, R free 0.280, DCC R free test set 1992 reflections (1.98%) DCC Wilson B-factor (Å 2 ) 73.0 Xtriage Anisotropy Xtriage Bulk solvent k sol (e/å 3 ), B sol (Å 2 ) 0.27, 12.8 EDS L-test for twinning 2 < L > = 0.40, < L 2 > = 0.23 Xtriage Estimated twinning fraction for h,-k,-l Xtriage F o,f c correlation 0.88 EDS Total number of atoms wwpdb-vp Average B, all atoms (Å 2 ) 90.0 wwpdb-vp Xtriage s analysis on translational NCS is as follows: The largest off-origin peak in the Patterson function is 2.60% of the height of the origin peak. No significant pseudotranslation is detected. 1 Intensities estimated from amplitudes. 2 Theoretical values of < L >, < L 2 > for acentric reflections are 0.5, respectively for untwinned datasets, and 0.375, 0.2 for perfectly twinned datasets.
18 Page 18 Full wwpdb X-ray Structure Validation Report 3KLE 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: GOL, MG, SWE, ZP4, 2DA, MRG 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 / /6357 (0.0%) 1 E / /6357 (0.0%) 1 I / / M / /6357 (0.0%) 2 B / / F / / J / / N / / C / /893 3 G / /893 3 K / /893 3 O / /893 4 D / /649 4 H / /649 4 L / /649 4 P / /649 All All / /50834 (0.0%) 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 3 C G K O D H 0 1 All All 0 6
19 Page 19 Full wwpdb X-ray Structure Validation Report 3KLE There are no bond length outliers. All (6) bond angle outliers are listed below: Mol Chain Res Type Atoms Z Observed( o ) Ideal( o ) 1 M 442 VAL CB-CA-C A 542 ILE CB-CA-C M 68 SER CB-CA-C A 463 ARG CB-CA-C E 492 GLU N-CA-C E 205 LEU CA-CB-CG There are no chirality outliers. All (6) planarity outliers are listed below: Mol Chain Res Type Group 3 C 705 DA Sidechain 4 D 820 DC Sidechain 3 G 705 DA Sidechain 4 H 820 DC Sidechain 3 K 705 DA Sidechain 3 O 705 DA Sidechain 5.2 Too-close contacts i In the following table, the Non-H and H(model) columns list the number of non-hydrogen atoms and hydrogen atoms in the chain respectively. The H(added) column lists the number of hydrogen atoms added and optimized by MolProbity. The Clashes column lists the number of clashes within the asymmetric unit, whereas Symm-Clashes lists symmetry related clashes. Mol Chain Non-H H(model) H(added) Clashes Symm-Clashes 1 A E I M B F J N C G K O D
20 Page 20 Full wwpdb X-ray Structure Validation Report 3KLE Mol Chain Non-H H(model) H(added) Clashes Symm-Clashes 4 H L P A E I M A E I M B F J A B C D E F G H I J K L M N O P 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 35. All (2498) close contacts within the same asymmetric unit are listed below, sorted by their clash magnitude. 1:I:441:TYR:CD1 1:I:544:GLY:HA :I:286:THR:O 1:I:287:LYS:HG :F:125:ARG:HD3 2:F:147:ASN:HA
21 Page 21 Full wwpdb X-ray Structure Validation Report 3KLE 1:I:489:SER:HB2 1:I:493:VAL:HG :B:79:GLU:HG3 2:B:83:ARG:HH :E:489:SER:HB2 1:E:493:VAL:HG :J:125:ARG:HD3 2:J:147:ASN:HA :E:511:ASP:OD1 1:E:512:LYS:HG :I:225:PRO:HB2 1:I:226:PRO:HD :M:489:SER:HB2 1:M:493:VAL:HG :A:489:SER:HB2 1:A:493:VAL:HG :B:125:ARG:HD3 2:B:147:ASN:HA :F:79:GLU:HG3 2:F:83:ARG:HH :E:441:TYR:CD1 1:E:544:GLY:HA :B:64:LYS:HE3 2:B:69:THR:HA :A:157:PRO:O 1:A:161:GLN:HG :N:65:LYS:HB2 2:N:68:SER:HB :N:125:ARG:HD3 2:N:147:ASN:HA :N:79:GLU:HG3 2:N:83:ARG:HH :F:64:LYS:HE3 2:F:69:THR:HA :M:511:ASP:OD1 1:M:512:LYS:HG :J:79:GLU:HG3 2:J:83:ARG:HH :J:184:MET:SD 2:J:410:TRP:HB :I:511:ASP:OD1 1:I:512:LYS:CG :I:511:ASP:OD1 1:I:512:LYS:HG :M:90:VAL:HG22 2:N:140:PRO:HB :B:79:GLU:HG3 2:B:83:ARG:NH :E:102:LYS:HD2 1:E:102:LYS:H :J:79:GLU:HG3 2:J:83:ARG:NH :I:274:ILE:HG23 1:I:306:ASN:HD :F:79:GLU:HG3 2:F:83:ARG:NH :I:441:TYR:HD1 1:I:544:GLY:HA :E:52:PRO:HA 1:E:143:ARG:HH :N:79:GLU:HG3 2:N:83:ARG:NH :A:23:GLN:NE2 1:A:60:VAL:H :A:102:LYS:HD2 1:A:102:LYS:H :J:5:ILE:HG13 2:J:6:GLU:H :I:439:THR:HG21 2:J:289:LEU:HD :M:274:ILE:HG23 1:M:306:ASN:HD :E:293:ILE:HD12 1:E:294:PRO:HD :E:277:ARG:NH1 1:E:336:GLN:HG :I:103:LYS:HE3 1:I:179:VAL:HG :M:23:GLN:NE2 1:M:60:VAL:H :M:439:THR:HG21 2:N:289:LEU:HD
22 Page 22 Full wwpdb X-ray Structure Validation Report 3KLE 1:M:102:LYS:HD2 1:M:102:LYS:H :I:67:ASN:O 1:I:68:SER:HB :J:5:ILE:HG13 2:J:6:GLU:N :A:52:PRO:HA 1:A:143:ARG:HH :J:79:GLU:CG 2:J:83:ARG:HH :B:79:GLU:CG 2:B:83:ARG:HH :J:24:TRP:CZ3 2:J:403:THR:HG :I:435:VAL:HA 2:J:290:THR:HG :M:225:PRO:HB2 1:M:226:PRO:HD :B:30:LYS:HE2 2:B:62:ALA:O :M:157:PRO:O 1:M:161:GLN:HG :I:293:ILE:HD12 1:I:294:PRO:HD :B:60:VAL:HG12 2:B:75:VAL:HG :A:293:ILE:HD12 1:A:294:PRO:HD :A:439:THR:HG21 2:B:289:LEU:HD :F:79:GLU:CG 2:F:83:ARG:HH :J:157:PRO:HG2 2:J:184:MET:HA :E:23:GLN:NE2 1:E:60:VAL:H :I:225:PRO:CB 1:I:226:PRO:HD :I:23:GLN:NE2 1:I:60:VAL:H :I:225:PRO:HB2 1:I:226:PRO:CD :N:79:GLU:CG 2:N:83:ARG:HH :N:60:VAL:HG12 2:N:75:VAL:HG :I:238:LYS:HG2 1:I:315:HIS:ND :E:157:PRO:O 1:E:161:GLN:HG :M:67:ASN:O 1:M:68:SER:HB :M:435:VAL:HA 2:N:290:THR:HG :F:60:VAL:HG12 2:F:75:VAL:HG :I:155:GLY:O 1:I:159:ILE:HG :M:135:ILE:H 1:M:135:ILE:HD :E:432:GLU:HG3 1:E:433:PRO:HD :I:558:LYS:HG2 1:I:559:VAL:H :F:244:ILE:HD13 2:F:244:ILE:H :I:277:ARG:NH1 1:I:336:GLN:HG :J:60:VAL:HG12 2:J:75:VAL:HG :N:64:LYS:HE3 2:N:69:THR:HA :B:111:VAL:HG11 2:B:187:LEU:HD :E:439:THR:HG21 2:F:289:LEU:HD :N:111:VAL:HG11 2:N:187:LEU:HD :A:260:LEU:HD21 1:A:303:LEU:HD :M:103:LYS:HE3 1:M:179:VAL:HG
23 Page 23 Full wwpdb X-ray Structure Validation Report 3KLE 1:A:432:GLU:HG3 1:A:433:PRO:HD :F:261:VAL:HG13 2:F:276:VAL:HG :I:157:PRO:O 1:I:161:GLN:HG :A:485:ALA:O 1:A:489:SER:HB :N:157:PRO:HG2 2:N:184:MET:HA :E:49:LYS:HE3 1:E:142:ILE:HD :M:432:GLU:HG3 1:M:433:PRO:HD :A:221:HIS:HE1 1:A:228:LEU:HB :F:30:LYS:HE2 2:F:62:ALA:O :B:244:ILE:HD13 2:B:244:ILE:H :A:135:ILE:H 1:A:135:ILE:HD :E:207:GLN:NE2 1:E:210:LEU:HD :N:96:HIS:HE1 2:N:381:VAL:O :F:111:VAL:HG11 2:F:187:LEU:HD :I:224:GLU:O 1:I:227:PHE:CE :I:382:ILE:O 2:J:136:ASN:HB :A:277:ARG:NH1 1:A:336:GLN:HG :F:100:LEU:H 2:F:100:LEU:HD :M:293:ILE:HD12 1:M:294:PRO:HD :A:171:PHE:HB2 1:A:208:HIS:CD :N:171:PHE:HB2 2:N:208:HIS:ND :E:529:GLU:O 1:E:530:LYS:HG :I:163:SER:O 1:I:167:ILE:HD :I:286:THR:C 1:I:287:LYS:HG :B:428:GLN:HG2 2:B:429:GLY:H :J:234:LEU:H 2:J:234:LEU:HD :I:224:GLU:O 1:I:227:PHE:CZ :F:157:PRO:HG2 2:F:184:MET:HA :B:13:LYS:O 2:B:16:MET:HB :E:485:ALA:O 1:E:489:SER:HB :E:220:LYS:O 1:E:220:LYS:HD :J:244:ILE:HD13 2:J:244:ILE:H :J:261:VAL:HG13 2:J:276:VAL:HG :B:157:PRO:HG2 2:B:184:MET:HA :I:135:ILE:HD12 1:I:135:ILE:H :I:432:GLU:HG3 1:I:433:PRO:HD :M:503:LEU:O 1:M:507:GLN:HG :J:171:PHE:HB2 2:J:208:HIS:ND :M:221:HIS:CE1 1:M:228:LEU:H :J:13:LYS:O 2:J:16:MET:HB :E:135:ILE:HD12 1:E:135:ILE:H
24 Page 24 Full wwpdb X-ray Structure Validation Report 3KLE 2:B:100:LEU:H 2:B:100:LEU:HD :B:171:PHE:HB2 2:B:208:HIS:ND :A:244:ILE:HD11 1:A:263:LYS:HG :E:458:VAL:HG12 1:E:548:VAL:HG :E:274:ILE:HG23 1:E:306:ASN:HD :I:558:LYS:HG2 1:I:559:VAL:N :N:261:VAL:HG13 2:N:276:VAL:HG :E:221:HIS:HE1 1:E:228:LEU:HB :M:277:ARG:NH1 1:M:336:GLN:HG :M:485:ALA:O 1:M:489:SER:HB :A:559:VAL:HG22 1:A:560:LEU:N :I:199:ARG:NH2 1:I:223:LYS:HB :M:23:GLN:HE21 1:M:60:VAL:H :M:253:THR:HG22 1:M:292:VAL:HG :N:96:HIS:CE1 2:N:381:VAL:O :A:274:ILE:HG23 1:A:306:ASN:HD :E:24:TRP:HB2 1:E:25:PRO:HD :F:13:LYS:O 2:F:16:MET:HB :I:485:ALA:O 1:I:489:SER:HB :I:503:LEU:O 1:I:507:GLN:HG :I:100:LEU:HD21 1:I:181:TYR:CE :I:458:VAL:HG12 1:I:548:VAL:HG :M:73:LYS:HE3 1:M:146:TYR:OH :A:3:SER:OG 1:A:5:ILE:HG :I:49:LYS:HE3 1:I:142:ILE:HD :I:260:LEU:HD21 1:I:303:LEU:HD :J:64:LYS:HE3 2:J:69:THR:HA :A:557:ARG:HD3 1:A:557:ARG:O :E:458:VAL:CG1 1:E:548:VAL:HG :E:510:PRO:HB2 1:E:522:ILE:HD :F:314:VAL:HG22 2:F:315:HIS:N :J:281:LYS:O 2:J:284:ARG:HB :J:5:ILE:HD11 8:J:438:SWE:H :A:171:PHE:HB2 1:A:208:HIS:HD :A:221:HIS:H 1:A:221:HIS:CD :A:27:THR:O 1:A:31:ILE:HG :E:500:GLN:HB3 2:F:422:LEU:HD :N:421:PRO:HA 2:N:426:TRP:HE :E:425:LEU:HD13 1:E:509:GLN:HE :N:13:LYS:O 2:N:16:MET:HB :E:503:LEU:O 1:E:507:GLN:HG
25 Page 25 Full wwpdb X-ray Structure Validation Report 3KLE 2:B:261:VAL:HG13 2:B:276:VAL:HG :N:69:THR:HG22 2:N:69:THR:O :A:511:ASP:OD1 1:A:512:LYS:HG :F:94:ILE:HD11 2:F:161:GLN:HG :F:281:LYS:O 2:F:284:ARG:HB :E:278:GLN:HG3 1:E:298:GLU:HB :J:3:SER:N 2:J:4:PRO:HD :B:281:LYS:O 2:B:284:ARG:HB :I:458:VAL:CG1 1:I:548:VAL:HG :E:103:LYS:HE3 1:E:179:VAL:HG :H:821:DC:H2 4:H:822:2DA:H :E:441:TYR:HD1 1:E:544:GLY:HA :J:30:LYS:HE2 2:J:62:ALA:O :B:194:GLU:OE2 2:B:195:ILE:HG :F:171:PHE:HB2 2:F:208:HIS:ND :A:503:LEU:O 1:A:507:GLN:HG :F:314:VAL:HG22 2:F:315:HIS:H :M:163:SER:O 1:M:167:ILE:HD :J:115:TYR:OH 2:J:157:PRO:HG :M:155:GLY:O 1:M:159:ILE:HG :B:314:VAL:HG22 2:B:315:HIS:N :A:103:LYS:HE3 1:A:179:VAL:HG :E:52:PRO:HA 1:E:143:ARG:NH :M:244:ILE:HD11 1:M:263:LYS:HG :N:303:LEU:HD21 2:N:307:ARG:HH :I:171:PHE:HB2 1:I:208:HIS:CD :J:421:PRO:HA 2:J:426:TRP:HE :B:94:ILE:HD11 2:B:161:GLN:HG :E:235:HIS:HB2 1:E:238:LYS:O :A:278:GLN:HG3 1:A:298:GLU:HB :A:155:GLY:O 1:A:159:ILE:HG :A:280:SER:O 1:A:283:LEU:HD :E:73:LYS:HE3 1:E:146:TYR:OH :F:421:PRO:HA 2:F:426:TRP:HE :J:303:LEU:HD21 2:J:307:ARG:HH :I:235:HIS:HB3 1:I:236:PRO:HD :I:441:TYR:CE1 1:I:544:GLY:HA :B:314:VAL:HG22 2:B:315:HIS:H :B:421:PRO:HA 2:B:426:TRP:HE :E:260:LEU:HD21 1:E:303:LEU:HD :J:314:VAL:HG22 2:J:315:HIS:H
26 Page 26 Full wwpdb X-ray Structure Validation Report 3KLE 1:A:49:LYS:HE3 1:A:142:ILE:HD :I:156:SER:N 1:I:157:PRO:HD :J:65:LYS:HA 2:J:407:GLN:HE :E:221:HIS:CE1 1:E:228:LEU:H :E:3:SER:OG 1:E:5:ILE:HG :N:65:LYS:HB2 2:N:68:SER:CB :A:27:THR:HB 1:A:30:LYS:HB :I:23:GLN:HE21 1:I:60:VAL:H :M:548:VAL:O 1:M:552:VAL:HG :J:314:VAL:HG22 2:J:315:HIS:N :E:463:ARG:HB2 1:E:463:ARG:NH :M:278:GLN:HG3 1:M:298:GLU:HB :C:709:DC:H2 3:C:710:DG:H :E:463:ARG:HH11 1:E:463:ARG:HB :N:387:PRO:HG2 2:N:389:PHE:CE :B:428:GLN:HG2 2:B:429:GLY:N :A:52:PRO:HA 1:A:143:ARG:NH :H:817:MRG:H2 4:H:818:DC:C :F:254:VAL:HG13 2:F:283:LEU:HD :E:102:LYS:HD2 1:E:102:LYS:N :E:548:VAL:O 1:E:552:VAL:HG :J:100:LEU:H 2:J:100:LEU:HD :A:72:ARG:HG3 1:A:151:GLN:HE :E:211:ARG:HD2 2:J:5:ILE:HD :I:24:TRP:HB2 1:I:25:PRO:HD :I:511:ASP:OD1 1:I:512:LYS:HG :B:33:ALA:O 2:B:37:ILE:HG :E:27:THR:HB 1:E:30:LYS:HB :N:281:LYS:O 2:N:284:ARG:HB :E:221:HIS:H 1:E:221:HIS:CD :F:303:LEU:HD21 2:F:307:ARG:HH :I:207:GLN:NE2 1:I:210:LEU:HD :I:463:ARG:HB2 1:I:463:ARG:HH :I:463:ARG:HB2 1:I:463:ARG:NH :N:314:VAL:HG22 2:N:315:HIS:N :A:31:ILE:O 1:A:35:VAL:HG :B:64:LYS:CE 2:B:69:THR:HG :F:194:GLU:OE2 2:F:195:ILE:HG :J:387:PRO:HG2 2:J:389:PHE:CE :N:314:VAL:HG22 2:N:315:HIS:H :E:244:ILE:HD11 1:E:263:LYS:HG
27 Page 27 Full wwpdb X-ray Structure Validation Report 3KLE 1:E:447:ASN:HB2 1:E:556:ILE:HG :I:510:PRO:HB2 1:I:522:ILE:HD :J:33:ALA:O 2:J:37:ILE:HG :I:228:LEU:HA 1:I:232:TYR:O :I:425:LEU:HD13 1:I:509:GLN:HE :J:254:VAL:HG13 2:J:283:LEU:HD :P:805:DG:H5 9:P:81:HOH:O :A:253:THR:HG22 1:A:292:VAL:HG :A:73:LYS:O 1:A:74:LEU:HD :M:511:ASP:OD1 1:M:512:LYS:CG :A:24:TRP:HB2 1:A:25:PRO:HD :A:458:VAL:HG13 1:A:548:VAL:HG :A:73:LYS:HE3 1:A:146:TYR:OH :B:64:LYS:HE3 2:B:69:THR:CA :B:369:THR:O 2:B:373:GLN:HG :I:101:LYS:CE 1:I:321:PRO:HG :N:100:LEU:H 2:N:100:LEU:HD :A:425:LEU:HD13 1:A:509:GLN:HE :A:156:SER:N 1:A:157:PRO:HD :A:510:PRO:HB2 1:A:522:ILE:HD :J:234:LEU:N 2:J:234:LEU:HD :I:229:TRP:CE2 1:I:230:MET:HG :M:510:PRO:HB2 1:M:522:ILE:HD :N:33:ALA:O 2:N:37:ILE:HG :M:90:VAL:CG2 2:N:140:PRO:HB :F:387:PRO:HG2 2:F:389:PHE:CE :B:75:VAL:HG11 2:B:77:PHE:CE :E:171:PHE:HB2 1:E:208:HIS:CD :B:74:LEU:HD12 2:B:75:VAL:N :C:708:DG:H2 3:C:709:DC:C :A:163:SER:O 1:A:167:ILE:HD :B:94:ILE:CD1 2:B:161:GLN:HG :A:320:ASP:OD2 1:A:323:LYS:HE :E:511:ASP:OD1 1:E:512:LYS:CG :I:101:LYS:HE3 1:I:321:PRO:CG :J:115:TYR:CZ 2:J:157:PRO:HG :I:90:VAL:HG23 2:J:141:GLY:O :F:33:ALA:O 2:F:37:ILE:HG :M:108:VAL:O 1:M:220:LYS:HB :F:94:ILE:CD1 2:F:161:GLN:HG :I:244:ILE:HD11 1:I:263:LYS:HG
28 Page 28 Full wwpdb X-ray Structure Validation Report 3KLE 1:I:27:THR:O 1:I:31:ILE:HG :I:286:THR:O 1:I:287:LYS:CG :K:709:DC:H2 3:K:710:DG:H :A:209:LEU:HB3 1:A:214:LEU:HB :A:221:HIS:H 1:A:221:HIS:HD :E:27:THR:O 1:E:31:ILE:HG :F:74:LEU:HD12 2:F:75:VAL:N :M:156:SER:N 1:M:157:PRO:HD :M:116:PHE:HA 1:M:148:VAL:HG :M:4:PRO:HD2 1:M:212:TRP:O :N:115:TYR:CZ 2:N:157:PRO:HG :N:194:GLU:OE2 2:N:195:ILE:HG :I:199:ARG:O 1:I:203:GLU:HG :I:100:LEU:CD2 1:I:181:TYR:CE :A:533:LEU:N 1:A:533:LEU:HD :D:817:MRG:H2 4:D:818:DC:C :I:2:ILE:H 1:I:2:ILE:HD :N:62:ALA:O 2:N:63:ILE:CG :A:548:VAL:O 1:A:552:VAL:HG :F:175:ASN:HD21 2:F:201:LYS:NZ :B:122:GLU:HA 2:B:125:ARG:HE :E:277:ARG:NH1 1:E:336:GLN:CG :I:223:LYS:HG3 1:I:223:LYS:O :N:244:ILE:HD13 2:N:244:ILE:H :A:329:ILE:HD11 1:A:375:ILE:HD :F:64:LYS:CE 2:F:69:THR:HG :I:469:LEU:HD21 1:I:480:GLN:HG :J:37:ILE:O 2:J:41:MET:HG :F:376:THR:O 2:F:380:ILE:HG :J:372:VAL:HG13 2:J:389:PHE:CE :E:221:HIS:CE1 1:E:228:LEU:HB :I:91:GLN:HG3 1:I:161:GLN:HE :I:329:ILE:HD11 1:I:375:ILE:HD :L:821:DC:H2 4:L:822:2DA:H :M:260:LEU:HD21 1:M:303:LEU:HD :I:439:THR:CG2 2:J:289:LEU:HD :A:23:GLN:HE21 1:A:60:VAL:H :B:387:PRO:HG2 2:B:389:PHE:CE :I:253:THR:HG22 1:I:292:VAL:HG :J:72:ARG:HH21 2:J:409:THR:HG :N:254:VAL:HG13 2:N:283:LEU:HD
29 Page 29 Full wwpdb X-ray Structure Validation Report 3KLE 2:F:100:LEU:H 2:F:100:LEU:CD :G:723:DC:H2 3:G:724:DT:O :I:548:VAL:O 1:I:552:VAL:HG :E:23:GLN:HE21 1:E:60:VAL:H :I:278:GLN:HG3 1:I:298:GLU:HB :I:101:LYS:HE3 1:I:321:PRO:HG :P:821:DC:H2 4:P:822:2DA:H :E:280:SER:O 1:E:283:LEU:HD :F:372:VAL:HG13 2:F:389:PHE:CE :I:435:VAL:CA 2:J:290:THR:HG :N:47:ILE:HG22 2:N:146:TYR:HA :E:394:GLN:HB2 1:E:397:THR:OG :I:303:LEU:O 1:I:307:ARG:HB :I:451:LYS:O 1:I:471:ASN:HA :M:458:VAL:HG13 1:M:548:VAL:HG :E:277:ARG:HH11 1:E:336:GLN:HG :I:558:LYS:HE3 1:I:559:VAL:O :I:238:LYS:HZ1 1:I:347:LYS:HE :A:366:LYS:O 1:A:370:GLU:HG :B:303:LEU:HD21 2:B:307:ARG:HH :E:451:LYS:O 1:E:471:ASN:HA :M:27:THR:O 1:M:31:ILE:HG :E:65:LYS:NZ 1:E:70:ARG:HH :I:441:TYR:CD1 1:I:544:GLY:CA :M:288:ALA:HB3 1:M:291:GLU:HG :M:451:LYS:O 1:M:471:ASN:HA :P:802:DA:H4 4:P:803:DC:OP :J:194:GLU:OE2 2:J:195:ILE:HG :J:94:ILE:HD11 2:J:161:GLN:HG :N:156:SER:HB2 2:N:157:PRO:HD :F:234:LEU:HD12 2:F:234:LEU:N :I:101:LYS:HE3 1:I:321:PRO:HD :J:243:PRO:HB2 2:J:244:ILE:HD :N:371:ALA:O 2:N:375:ILE:HG :B:372:VAL:HG13 2:B:389:PHE:CE :M:329:ILE:HD11 1:M:375:ILE:HD :M:469:LEU:HD21 1:M:480:GLN:HG :N:78:ARG:HD3 2:N:411:ILE:HB :B:254:VAL:HG13 2:B:283:LEU:HD :E:366:LYS:O 1:E:370:GLU:HG :E:3:SER:HB3 1:E:119:PRO:HD
30 Page 30 Full wwpdb X-ray Structure Validation Report 3KLE 1:E:469:LEU:HD21 1:E:480:GLN:HG :F:100:LEU:N 2:F:100:LEU:HD :G:709:DC:H2 3:G:710:DG:H :M:303:LEU:O 1:M:307:ARG:HB :A:135:ILE:HD12 1:A:135:ILE:N :F:356:ARG:HG2 2:F:357:MET:H :F:37:ILE:O 2:F:41:MET:HG :N:31:ILE:O 2:N:35:VAL:HG :E:171:PHE:HB2 1:E:208:HIS:HD :J:376:THR:HG23 2:J:386:THR:HG :N:369:THR:O 2:N:373:GLN:HG :J:371:ALA:O 2:J:375:ILE:HG :A:237:ASP:OD2 1:A:238:LYS:HD :N:122:GLU:HA 2:N:125:ARG:HE :I:209:LEU:HB3 1:I:214:LEU:HB :B:100:LEU:H 2:B:100:LEU:CD :M:209:LEU:HB3 1:M:214:LEU:HB :F:376:THR:HG23 2:F:386:THR:HG :P:818:DC:H2 4:P:819:DG:H :A:102:LYS:HD2 1:A:102:LYS:N :A:235:HIS:HB2 1:A:238:LYS:O :A:90:VAL:HG22 2:B:140:PRO:HB :B:376:THR:O 2:B:380:ILE:HG :C:709:DC:H2 3:C:710:DG:C :G:708:DG:H2 3:G:709:DC:C :P:818:DC:H2 4:P:819:DG:C :E:132:ILE:O 1:E:141:GLY:HA :E:148:VAL:O 1:E:150:PRO:HD :I:103:LYS:HE3 1:I:179:VAL:CG :J:31:ILE:O 2:J:35:VAL:HG :A:227:PHE:HB2 1:A:234:LEU:HB :E:317:VAL:HG11 1:E:347:LYS:HB :L:818:DC:H2 4:L:819:DG:C :N:376:THR:HG23 2:N:386:THR:HG :L:818:DC:H2 4:L:819:DG:H :N:184:MET:SD 2:N:410:TRP:HB :A:70:ARG:HH12 6:A:823:ZP4:C :A:221:HIS:CD2 1:A:221:HIS:N :E:227:PHE:HB2 1:E:234:LEU:HB :E:329:ILE:HD11 1:E:375:ILE:HD :M:425:LEU:HD13 1:M:509:GLN:HE
31 Page 31 Full wwpdb X-ray Structure Validation Report 3KLE 1:M:94:ILE:HD11 3:O:708:DG:H :A:135:ILE:H 1:A:135:ILE:CD :E:303:LEU:O 1:E:307:ARG:HB :F:64:LYS:HE3 2:F:69:THR:CA :G:705:DA:H2 3:G:706:DT:O :A:451:LYS:O 1:A:471:ASN:HA :A:559:VAL:HG22 1:A:560:LEU:H :E:136:ASN:OD1 1:E:138:GLU:HG :E:277:ARG:HH11 1:E:336:GLN:CG :J:156:SER:HB2 2:J:157:PRO:HD :J:107:THR:HG23 2:J:232:TYR:HE :A:148:VAL:O 1:A:150:PRO:HD :B:7:THR:HG22 2:B:119:PRO:HG :D:802:DA:H4 4:D:803:DC:OP :I:280:SER:O 1:I:283:LEU:HD :J:72:ARG:HH22 2:J:151:GLN:HB :M:184:MET:HG3 4:P:822:2DA:H :A:518:VAL:O 1:A:522:ILE:HG :M:556:ILE:HG13 1:M:557:ARG:N :E:22:LYS:HG2 1:E:23:GLN:N :A:559:VAL:CG2 1:A:560:LEU:N :E:463:ARG:HH11 1:E:463:ARG:CB :F:75:VAL:HG11 2:F:77:PHE:CE :J:66:LYS:O 2:J:67:ASP:HB :M:135:ILE:N 1:M:135:ILE:HD :A:235:HIS:HB3 1:A:236:PRO:HD :E:435:VAL:HA 2:F:290:THR:HG :J:125:ARG:HG2 2:J:146:TYR:O :B:371:ALA:O 2:B:375:ILE:HG :F:369:THR:O 2:F:373:GLN:HG :I:195:ILE:O 1:I:199:ARG:HG :I:394:GLN:HB2 1:I:397:THR:OG :J:369:THR:O 2:J:373:GLN:HG :M:135:ILE:CD1 1:M:135:ILE:H :J:6:GLU:HA 2:J:6:GLU:OE :B:153:TRP:CE2 2:B:155:GLY:HA :F:314:VAL:CG2 2:F:315:HIS:H :N:171:PHE:HB2 2:N:208:HIS:CE :J:403:THR:HG23 9:J:449:HOH:O :M:116:PHE:HA 1:M:148:VAL:CG :N:72:ARG:NH1 2:N:151:GLN:OE
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