full wwpdb x-ray structure validation report o i...page 6 ufll wwpdb x-ray structure alidationv...

Full wwPDB X-ray Structure Validation Report iO

May 16, 2020 � 11:59 pm BST

PDB ID : 3UPNTitle : Structure of penicillin-binding protein A from M. tuberculosis: imipenem acyl-

enzyme complexAuthors : Davies, C.; Fedorovich, A.

Deposited on : 2011-11-18Resolution : 2.20 Å(reported)

This is a Full wwPDB X-ray Structure Validation Report for a publicly released PDB entry.

We welcome your comments at [email protected] user guide is available at

https://www.wwpdb.org/validation/2017/XrayValidationReportHelpwith speci�c help available everywhere you see the iO symbol.

The following versions of software and data (see references iO) were used in the production of this report:

MolProbity : 4.02b-467Mogul : 1.8.5 (274361), CSD as541be (2020)

Xtriage (Phenix) : 1.13EDS : 2.11

buster-report : 1.1.7 (2018)Percentile statistics : 20191225.v01 (using entries in the PDB archive December 25th 2019)

Refmac : 5.8.0158CCP4 : 7.0.044 (Gargrove)

Ideal geometry (proteins) : Engh & Huber (2001)Ideal geometry (DNA, RNA) : Parkinson et al. (1996)

Validation Pipeline (wwPDB-VP) : 2.11

https://www.wwpdb.org/validation/2017/XrayValidationReportHelp



https://www.wwpdb.org/validation/2017/XrayValidationReportHelp#references

Full wwPDB X-ray Structure Validation Report 3UPN

1 Overall quality at a glance iO

The following experimental techniques were used to determine the structure:X-RAY DIFFRACTION

The reported resolution of this entry is 2.20 Å.

Percentile scores (ranging between 0-100) for global validation metrics of the entry are shown inthe following graphic. The table shows the number of entries on which the scores are based.

MetricWhole archive(#Entries)

Similar resolution(#Entries, resolution range(Å))

Rfree 130704 4898 (2.20-2.20)Clashscore 141614 5594 (2.20-2.20)

Ramachandran outliers 138981 5503 (2.20-2.20)Sidechain outliers 138945 5504 (2.20-2.20)RSRZ outliers 127900 4800 (2.20-2.20)

The table below summarises the geometric issues observed across the polymeric chains and their�t to the electron density. The red, orange, yellow and green segments on the lower bar indicatethe fraction of residues that contain outliers for >=3, 2, 1 and 0 types of geometric qualitycriteria respectively. 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 dotrepresenting fractions <=5% The upper red bar (where present) indicates the fraction of residuesthat have poor �t to the electron density. The numeric value is given above the bar.

Mol Chain Length Quality of chain

1 A 462

1 B 462

https://www.wwpdb.org/validation/2017/XrayValidationReportHelp#overall_quality


2 Entry composition iO

There are 3 unique types of molecules in this entry. The entry contains 6525 atoms, of which 0are hydrogens and 0 are deuteriums.

In the tables below, the ZeroOcc column contains the number of atoms modelled with zero occu-pancy, the AltConf column contains the number of residues with at least one atom in alternateconformation and the Trace column contains the number of residues modelled with at most 2atoms.

� Molecule 1 is a protein called Penicillin-binding protein A.

Mol Chain Residues Atoms ZeroOcc AltConf Trace

1 A 435Total C N O S3214 2015 573 617 9

0 0 0

1 B 436Total C N O S3214 2013 574 618 9

0 0 0

There are 12 discrepancies between the modelled and reference sequences:

Chain Residue Modelled Actual Comment ReferenceA 30 GLY - EXPRESSION TAG UNP P71586A 31 ALA - EXPRESSION TAG UNP P71586A 32 MET - EXPRESSION TAG UNP P71586A 33 GLY - EXPRESSION TAG UNP P71586A 34 SER - EXPRESSION TAG UNP P71586A 384 ARG GLY SEE REMARK 999 UNP P71586B 30 GLY - EXPRESSION TAG UNP P71586B 31 ALA - EXPRESSION TAG UNP P71586B 32 MET - EXPRESSION TAG UNP P71586B 33 GLY - EXPRESSION TAG UNP P71586B 34 SER - EXPRESSION TAG UNP P71586B 384 ARG GLY SEE REMARK 999 UNP P71586

� Molecule 2 is (5R)-5-[(1S,2R)-1-formyl-2-hydroxypropyl]-3-[(2-{[(E)-iminomethyl]amino}ethyl)sulfanyl]-4,5-dihydro-1H-pyrrole-2-carboxylic acid (three-letter code: IM2) (formula:C12H19N3O4S).

https://www.wwpdb.org/validation/2017/XrayValidationReportHelp#entry_composition


Mol Chain Residues Atoms ZeroOcc AltConf

2 A 1Total C N O S20 12 3 4 1

0 0

2 B 1Total C N O S20 12 3 4 1

0 0

� Molecule 3 is water.

Mol Chain Residues Atoms ZeroOcc AltConf

3 A 31Total O31 31

0 0

3 B 26Total O26 26

0 0


3 Residue-property plots iO

These plots are drawn for all protein, RNA and DNA chains in the entry. The �rst graphic fora 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 theycontain at least one outlier: green = 0, yellow = 1, orange = 2 and red = 3 or more. A red dotabove a residue indicates a poor �t to the electron density (RSRZ > 2). Stretches of 2 or moreconsecutive residues without any outlier are shown as a green connector. Residues present in thesample, but not in the model, are shown in grey.

• Molecule 1: Penicillin-binding protein A

Chain A:

GLY

ALA

MET

GLY

SER

ARG

ALA

ASP

PRO

ARG

ASN

GLN

ARG

VAL

L44•

L45•

D46•

E47•

Y48•

Q51

R52

G53

F74

Y84

G89

F90

Y91

A99

L115

F116•

R119•

F123•

G126•

R127

G132

N139

I142

Q143

Y155

G170

E192

Q199

D203•

S222

T223•

V226•

I227•

T240

A246•

P247•

T248

L251•

T255•

A256•

Q257•

L258

Y261•

G262•

G263•

A264•

D268•

S281

R292

L307

P310

P311

A330•

T335

K340

D341

V342

A343

L344

L347•

A348•

N349•

A350•

E351

I352•

A353•

A357

M363

R364

P365

D375•

L376

I379

V383•

Q386

Q387

G418•

T425

G426

G431•

T432•

ASP

PRO

ARG

HIS

T437•

P438

P439

Y443

I444•

A445•

F446

A457•

R466

LEU

SER

ALA

THR

GLY

GLY

A473

L474

Q488

GLY

GLU

PRO

• Molecule 1: Penicillin-binding protein A

Chain B:

GLY

ALA

MET

GLY

SER

ARG

ALA

ASP

PRO

ARG

ASN

GLN

ARG

VAL

LEU

LEU

D46•

E47•

Y48•

S49

R50

G53

A67

R73

V83

Y84

R113

R118

R119

F123•

F124

T125

G126

R127

D128

G132

N139

I142

Q143

W147

Y155

V162

G170

V176

Q199

P205•

P219

S222

E241

T248

L258

E269

P270

T271

V272

S273

L274

R292

R303

L307

P313

T314

T335

V342

A343

L344•

L347•

A350•

R364

P365

D375

V383•

R384

R388

V404

K408

P417•

G426

T427

A428

E429

H430

GLY

THR

ASP

PRO

ARG

HIS

THR

P438

A457•

V458•

A469•

T470

G471

L474

I478

V482

Q488

GLY

GLU

PRO

https://www.wwpdb.org/validation/2017/XrayValidationReportHelp#residue_plots


4 Data and re�nement statistics iO

Property Value SourceSpace group P 61 DepositorCell constantsa, b, c, α, β, γ

122.80Å 122.80Å 101.10Å90.00◦ 90.00◦ 120.00◦

Depositor

Resolution (Å)37.35 � 2.2037.35 � 2.20

DepositorEDS

% Data completeness(in resolution range)

99.1 (37.35-2.20)99.1 (37.35-2.20)

DepositorEDS

Rmerge 0.07 DepositorRsym (Not available) Depositor

< I/σ(I) > 1 3.09 (at 2.20Å) XtriageRe�nement program REFMAC Depositor

R, Rfree0.214 , 0.2580.209 , 0.256

DepositorDCC

Rfree test set 2149 re�ections (4.94%) wwPDB-VPWilson B-factor (Å2) 42.7 Xtriage

Anisotropy 0.640 XtriageBulk solvent ksol(e/Å3), Bsol(Å2) 0.35 , 37.1 EDS

L-test for twinning2 < |L| > = 0.51, < L2 > = 0.34 XtriageEstimated twinning fraction 0.032 for h,-h-k,-l Xtriage

Fo,Fc correlation 0.95 EDSTotal number of atoms 6525 wwPDB-VP

Average B, all atoms (Å2) 46.0 wwPDB-VP

Xtriage's analysis on translational NCS is as follows: The largest o�-origin peak in the Patterson

function is 4.05% of the height of the origin peak. No signi�cant pseudotranslation is detected.

1Intensities estimated from amplitudes.2Theoretical values of < |L| >, < L2 > for acentric re�ections are 0.5, 0.333 respectively for untwinned datasets,

and 0.375, 0.2 for perfectly twinned datasets.

https://www.wwpdb.org/validation/2017/XrayValidationReportHelp#data_stats


5 Model quality iO

5.1 Standard geometry iO

Bond lengths and bond angles in the following residue types are not validated in this section:IM2

The Z score for a bond length (or angle) is the number of standard deviations the observed valueis removed from the expected value. A bond length (or angle) with |Z| > 5 is considered anoutlier worth inspection. RMSZ is the root-mean-square of all Z scores of the bond lengths (orangles).

Mol ChainBond lengths Bond anglesRMSZ #|Z| >5 RMSZ #|Z| >5

1 A 0.51 0/3280 0.60 0/44781 B 0.51 0/3281 0.61 0/4479All All 0.51 0/6561 0.60 0/8957

There are no bond length outliers.

There are no bond angle outliers.

There are no chirality outliers.

There are no planarity outliers.

5.2 Too-close contacts iO

In the following table, the Non-H and H(model) columns list the number of non-hydrogen atomsand hydrogen atoms in the chain respectively. The H(added) column lists the number of hydrogenatoms added and optimized by MolProbity. The Clashes column lists the number of clashes withinthe asymmetric unit, whereas Symm-Clashes lists symmetry related clashes.

Mol Chain Non-H H(model) H(added) Clashes Symm-Clashes1 A 3214 0 3209 30 01 B 3214 0 3206 25 12 A 20 0 14 0 02 B 20 0 14 3 03 A 31 0 0 0 03 B 26 0 0 0 0All All 6525 0 6443 54 1

The all-atom clashscore is de�ned as the number of clashes found per 1000 atoms (includinghydrogen atoms). The all-atom clashscore for this structure is 4.

All (54) close contacts within the same asymmetric unit are listed below, sorted by their clash

https://www.wwpdb.org/validation/2017/XrayValidationReportHelp#model_quality

https://www.wwpdb.org/validation/2017/XrayValidationReportHelp#standard_geometry

https://www.wwpdb.org/validation/2017/XrayValidationReportHelp#close_contacts


magnitude.

Atom-1 Atom-2Interatomicdistance (Å)

Clashoverlap (Å)

1:A:292:ARG:HG3 1:A:292:ARG:HH11 1.46 0.791:B:427:THR:HG23 2:B:800:IM2:H222 1.68 0.741:B:427:THR:CG2 2:B:800:IM2:H222 2.23 0.691:A:292:ARG:CG 1:A:292:ARG:HH11 2.09 0.651:B:50:ARG:HH22 1:B:119:ARG:HD2 1.63 0.641:B:314:THR:HA 1:B:364:ARG:NH2 2.13 0.631:B:125:THR:HG23 1:B:127:ARG:HG3 1.85 0.581:A:199:GLN:NE2 1:A:203:ASP:OD2 2.39 0.551:B:170:GLY:O 1:B:365:PRO:HA 2.08 0.53

1:B:269:GLU:HB3 1:B:270:PRO:HD2 1.90 0.531:A:307:LEU:HD21 1:A:344:LEU:HD11 1.91 0.531:B:73:ARG:HH21 1:B:73:ARG:HG2 1.74 0.521:A:364:ARG:HB2 1:A:387:GLN:HG3 1.90 0.521:A:261:TYR:OH 1:A:466:ARG:HA 2.11 0.511:A:222:SER:HB2 1:A:426:GLY:HA3 1.94 0.491:A:292:ARG:NH1 1:A:292:ARG:HG3 2.19 0.491:A:335:THR:HG23 1:A:342:VAL:CG2 2.42 0.491:A:425:THR:HG22 1:A:443:TYR:HD1 1.78 0.481:B:139:ASN:HB3 1:B:142:ILE:HD12 1.93 0.481:A:155:TYR:HH 1:B:155:TYR:HH 1.62 0.471:A:340:LYS:HE3 1:A:341:ASP:OD2 2.13 0.471:B:67:ALA:HB1 1:B:73:ARG:NH1 2.30 0.471:A:261:TYR:HA 1:A:262:GLY:HA2 1.71 0.461:A:53:GLY:HA3 1:A:132:GLY:O 2.16 0.461:B:313:PRO:O 1:B:364:ARG:NH2 2.49 0.45

1:B:307:LEU:HD21 1:B:344:LEU:HD11 1.99 0.451:B:303:ARG:HA 1:B:307:LEU:O 2.17 0.441:B:335:THR:HG23 1:B:342:VAL:CG2 2.47 0.441:A:116:PHE:HD2 1:A:119:ARG:NH1 2.14 0.441:B:219:PRO:HB2 1:B:428:ALA:HB1 2.00 0.441:A:363:MET:SD 1:A:386:GLN:HG2 2.58 0.441:A:115:LEU:HD21 1:A:379:ILE:HD11 1.99 0.441:B:162:VAL:HB 1:B:176:VAL:HB 2.00 0.431:A:84:TYR:CE2 1:A:143:GLN:HG2 2.53 0.431:A:357:ALA:HB2 1:A:446:PHE:CG 2.53 0.431:A:170:GLY:O 1:A:365:PRO:HA 2.18 0.431:B:53:GLY:HA3 1:B:132:GLY:O 2.18 0.431:A:116:PHE:HD2 1:A:119:ARG:HH12 1.66 0.421:A:222:SER:HB2 1:A:426:GLY:CA 2.49 0.421:A:47:GLU:OE2 1:A:91:TYR:OH 2.35 0.421:B:471:GLY:HA2 2:B:800:IM2:H232 1.99 0.42

Continued on next page...


Continued from previous page...


Clashoverlap (Å)

1:A:438:PRO:HA 1:A:439:PRO:HD3 1.97 0.421:A:246:ALA:HA 1:A:247:PRO:HD3 1.94 0.421:A:89:GLY:HA3 1:A:99:ALA:HB3 2.00 0.421:A:375:ASP:O 1:A:376:LEU:HB2 2.19 0.421:B:314:THR:HA 1:B:364:ARG:HH22 1.84 0.421:A:310:PRO:HA 1:A:311:PRO:HD3 1.97 0.421:B:478:ILE:O 1:B:482:VAL:HG23 2.19 0.42

1:A:51:GLN:HB2 1:A:74:PHE:CZ 2.55 0.421:B:83:VAL:HG22 1:B:147:TRP:CD1 2.54 0.411:B:222:SER:HB2 1:B:426:GLY:HA2 2.02 0.411:B:84:TYR:CE2 1:B:143:GLN:HG2 2.56 0.411:B:404:VAL:HG12 1:B:408:LYS:HE2 2.01 0.411:A:139:ASN:HB3 1:A:142:ILE:HD12 2.02 0.41

All (1) symmetry-related close contacts are listed below. The label for Atom-2 includes the sym-metry operator and encoded unit-cell translations to be applied.


Clashoverlap (Å)

1:B:113:ARG:NH1 1:B:375:ASP:OD1[6_445] 2.14 0.06

5.3 Torsion angles iO

5.3.1 Protein backbone iO

In the following table, the Percentiles column shows the percent Ramachandran outliers of thechain as a percentile score with respect to all X-ray entries followed by that with respect to entriesof similar resolution.

The Analysed column shows the number of residues for which the backbone conformation wasanalysed, and the total number of residues.

Mol Chain Analysed Favoured Allowed Outliers Percentiles

1 A 429/462 (93%) 418 (97%) 11 (3%) 0 100 100

1 B 432/462 (94%) 421 (98%) 11 (2%) 0 100 100

All All 861/924 (93%) 839 (97%) 22 (3%) 0 100 100

There are no Ramachandran outliers to report.

https://www.wwpdb.org/validation/2017/XrayValidationReportHelp#torsion_angles

https://www.wwpdb.org/validation/2017/XrayValidationReportHelp#protein_backbone


5.3.2 Protein sidechains iO

In the following table, the Percentiles column shows the percent sidechain outliers of the chain as apercentile score with respect to all X-ray entries followed by that with respect to entries of similarresolution.

The Analysed column shows the number of residues for which the sidechain conformation wasanalysed, and the total number of residues.

Mol Chain Analysed Rotameric Outliers Percentiles

1 A 331/350 (95%) 320 (97%) 11 (3%) 38 49

1 B 330/350 (94%) 315 (96%) 15 (4%) 27 34

All All 661/700 (94%) 635 (96%) 26 (4%) 32 41

All (26) residues with a non-rotameric sidechain are listed below:

Mol Chain Res Type1 A 127 ARG1 A 192 GLU1 A 240 THR1 A 248 THR1 A 258 LEU1 A 268 ASP1 A 281 SER1 A 292 ARG1 A 383 VAL1 A 437 THR1 A 474 LEU1 B 73 ARG1 B 118 ARG1 B 125 THR1 B 128 ASP1 B 199 GLN1 B 241 GLU1 B 248 THR1 B 258 LEU1 B 272 VAL1 B 274 LEU1 B 292 ARG1 B 364 ARG1 B 384 ARG1 B 388 ARG1 B 474 LEU

https://www.wwpdb.org/validation/2017/XrayValidationReportHelp#protein_sidechains


Some sidechains can be �ipped to improve hydrogen bonding and reduce clashes. All (3) suchsidechains are listed below:

Mol Chain Res Type1 B 189 HIS1 B 242 GLN1 B 488 GLN

5.3.3 RNA iO

There are no RNA molecules in this entry.

5.4 Non-standard residues in protein, DNA, RNA chains iO

There are no non-standard protein/DNA/RNA residues in this entry.

5.5 Carbohydrates iO

There are no carbohydrates in this entry.

5.6 Ligand geometry iO

2 ligands are modelled in this entry.

In the following table, the Counts columns list the number of bonds (or angles) for which Mogulstatistics could be retrieved, the number of bonds (or angles) that are observed in the model andthe number of bonds (or angles) that are de�ned in the Chemical Component Dictionary. TheLink column lists molecule types, if any, to which the group is linked. The Z score for a bondlength (or angle) is the number of standard deviations the observed value is removed from theexpected value. A bond length (or angle) with |Z| > 2 is considered an outlier worth inspection.RMSZ is the root-mean-square of all Z scores of the bond lengths (or angles).

Mol Type Chain Res LinkBond lengths Bond angles

Counts RMSZ #|Z| > 2 Counts RMSZ #|Z| > 2

2 IM2 B 800 1 13,20,20 1.78 2 (15%) 7,26,26 2.76 2 (28%)

2 IM2 A 800 1 13,20,20 1.94 3 (23%) 7,26,26 2.59 3 (42%)

In the following table, the Chirals column lists the number of chiral outliers, the number of chiralcenters analysed, the number of these observed in the model and the number de�ned in theChemical Component Dictionary. Similar counts are reported in the Torsion and Rings columns.'-' means no outliers of that kind were identi�ed.

https://www.wwpdb.org/validation/2017/XrayValidationReportHelp#rna

https://www.wwpdb.org/validation/2017/XrayValidationReportHelp#nonstandard_residues_and_ligands




Mol Type Chain Res Link Chirals Torsions Rings2 IM2 B 800 1 - 9/13/32/32 0/1/1/1

2 IM2 A 800 1 - 8/13/32/32 0/1/1/1

All (5) bond length outliers are listed below:

Mol Chain Res Type Atoms Z Observed(Å) Ideal(Å)2 A 800 IM2 C25-N24 -4.75 1.22 1.342 B 800 IM2 C25-N24 -4.24 1.24 1.342 B 800 IM2 C31-C3 -3.88 1.46 1.522 A 800 IM2 C31-C3 -3.77 1.46 1.522 A 800 IM2 C6-C7 2.37 1.54 1.50

All (5) bond angle outliers are listed below:

Mol Chain Res Type Atoms Z Observed(o) Ideal(o)2 B 800 IM2 C22-S21-C2 6.15 114.03 103.942 A 800 IM2 C22-S21-C2 5.00 112.13 103.942 B 800 IM2 C22-C23-N24 -3.11 105.92 112.392 A 800 IM2 C22-C23-N24 -2.98 106.19 112.392 A 800 IM2 O7-C7-C6 -2.95 117.77 125.23

There are no chirality outliers.

All (17) torsion outliers are listed below:

Mol Chain Res Type Atoms2 B 800 IM2 C1-C5-C6-C72 B 800 IM2 C1-C5-C6-C612 B 800 IM2 C7-C6-C61-O622 B 800 IM2 C7-C6-C61-C622 B 800 IM2 C5-C6-C61-O622 B 800 IM2 C5-C6-C61-C622 A 800 IM2 C1-C2-S21-C222 A 800 IM2 C1-C5-C6-C72 A 800 IM2 C7-C6-C61-O622 A 800 IM2 C7-C6-C61-C622 A 800 IM2 C5-C6-C61-C622 A 800 IM2 C5-C6-C61-O622 B 800 IM2 C3-C2-S21-C222 A 800 IM2 C5-C6-C7-O72 B 800 IM2 S21-C22-C23-N242 B 800 IM2 C23-C22-S21-C22 A 800 IM2 C23-C22-S21-C2


There are no ring outliers.

1 monomer is involved in 3 short contacts:

Mol Chain Res Type Clashes Symm-Clashes2 B 800 IM2 3 0

The following is a two-dimensional graphical depiction of Mogul quality analysis of bond lengths,bond angles, torsion angles, and ring geometry for all instances of the Ligand of Interest. Inaddition, ligands with molecular weight > 250 and outliers as shown on the validation Tables willalso be included. For torsion angles, if less then 5% of the Mogul distribution of torsion angles iswithin 10 degrees of the torsion angle in question, then that torsion angle is considered an outlier.Any bond that is central to one or more torsion angles identi�ed as an outlier by Mogul will behighlighted in the graph. For rings, the root-mean-square deviation (RMSD) between the ringin question and similar rings identi�ed by Mogul is calculated over all ring torsion angles. If theaverage RMSD is greater than 60 degrees and the minimal RMSD between the ring in question andany Mogul-identi�ed rings is also greater than 60 degrees, then that ring is considered an outlier.The outliers are highlighted in purple. The color gray indicates Mogul did not �nd su�cientequivalents in the CSD to analyse the geometry.

Ligand IM2 B 800

Bond lengths Bond angles

Torsions Rings


Ligand IM2 A 800

Bond lengths Bond angles

Torsions Rings

5.7 Other polymers iO

There are no such residues in this entry.

5.8 Polymer linkage issues iO

There are no chain breaks in this entry.


https://www.wwpdb.org/validation/2017/XrayValidationReportHelp#polymer_linkage


6 Fit of model and data iO

6.1 Protein, DNA and RNA chains iO

In the following table, the column labelled `#RSRZ> 2' contains the number (and percentage)of RSRZ outliers, followed by percent RSRZ outliers for the chain as percentile scores relative toall X-ray entries and entries of similar resolution. The OWAB column contains the minimum,median, 95th percentile and maximum values of the occupancy-weighted average B-factor perresidue. The column labelled `Q< 0.9' lists the number of (and percentage) of residues with anaverage occupancy less than 0.9.

Mol Chain Analysed <RSRZ> #RSRZ>2 OWAB(Å2) Q<0.9

1 A 435/462 (94%) 0.26 40 (9%) 9 7 28, 44, 70, 84 0

1 B 436/462 (94%) 0.01 13 (2%) 50 48 31, 44, 63, 78 0

All All 871/924 (94%) 0.14 53 (6%) 21 20 28, 44, 66, 84 0

All (53) RSRZ outliers are listed below:

Mol Chain Res Type RSRZ1 A 256 ALA 5.71 B 47 GLU 4.51 A 255 THR 4.41 A 432 THR 4.01 B 48 TYR 3.91 A 268 ASP 3.91 A 251 LEU 3.51 A 437 THR 3.41 A 352 ILE 3.31 A 383 VAL 3.31 B 469 ALA 3.21 A 261 TYR 3.11 A 350 ALA 3.11 A 347 LEU 3.11 A 349 ASN 3.11 A 119 ARG 3.11 A 44 LEU 3.01 B 123 PHE 2.91 B 417 PRO 2.91 A 375 ASP 2.91 A 444 ILE 2.81 A 116 PHE 2.81 B 350 ALA 2.81 A 247 PRO 2.8

Continued on next page...

https://www.wwpdb.org/validation/2017/XrayValidationReportHelp#fit_model_data

https://www.wwpdb.org/validation/2017/XrayValidationReportHelp#fit_protein_na_chains


Continued from previous page...

Mol Chain Res Type RSRZ1 A 264 ALA 2.71 A 45 LEU 2.71 A 418 GLY 2.71 A 348 ALA 2.61 B 457 ALA 2.61 A 263 GLY 2.61 A 431 GLY 2.51 A 457 ALA 2.51 A 46 ASP 2.31 A 330 ALA 2.31 A 353 ALA 2.31 A 123 PHE 2.31 A 47 GLU 2.31 A 262 GLY 2.31 A 203 ASP 2.21 A 257 GLN 2.21 B 458 VAL 2.21 A 445 ALA 2.21 B 205 PRO 2.11 A 226 VAL 2.11 A 126 GLY 2.11 A 223 THR 2.11 B 383 VAL 2.11 A 246 ALA 2.11 A 48 TYR 2.11 A 227 ILE 2.01 B 344 LEU 2.01 B 347 LEU 2.01 B 46 ASP 2.0

6.2 Non-standard residues in protein, DNA, RNA chains iO

There are no non-standard protein/DNA/RNA residues in this entry.

6.3 Carbohydrates iO

There are no carbohydrates in this entry.

https://www.wwpdb.org/validation/2017/XrayValidationReportHelp#fit_nonstandard_and_ligands



6.4 Ligands iO

In the following table, the Atoms column lists the number of modelled atoms in the group and thenumber de�ned in the chemical component dictionary. The B-factors column lists the minimum,median, 95th percentile and maximum values of B factors of atoms in the group. The columnlabelled `Q< 0.9' lists the number of atoms with occupancy less than 0.9.

Mol Type Chain Res Atoms RSCC RSR B-factors(Å2) Q<0.92 IM2 A 800 20/20 0.75 0.18 56,66,69,69 02 IM2 B 800 20/20 0.78 0.23 53,64,69,70 0

The following is a graphical depiction of the model �t to experimental electron density of allinstances of the Ligand of Interest. In addition, ligands with molecular weight > 250 and outliersas shown on the geometry validation Tables will also be included. Each �t is shown from di�erentorientation to approximate a three-dimensional view.

Electron density around IM2 A 800:

2mFo-DFc (at 0.7 rmsd) in gray

mFo-DFc (at 3 rmsd) in purple (negative)

and green (positive)



Electron density around IM2 B 800:

2mFo-DFc (at 0.7 rmsd) in gray

mFo-DFc (at 3 rmsd) in purple (negative)

and green (positive)

6.5 Other polymers iO

There are no such residues in this entry.


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