full wwpdb x-ray structure validation report...

Full wwPDB X-ray Structure Validation Report i○

Mar 14, 2018 – 01:19 pm GMT

PDB ID : 1Q84Title : Crystal structure of the mouse acetylcholinesterase-TZ2PA6 anti complex

Authors : Bourne, Y.; Kolb, H.C.; Radic, Z.; Sharpless, K.B.; Taylor, P.; Marchot, P.Deposited on : 2003-08-20

Resolution : 2.45 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 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-467Mogul : 1.7.3 (157068), CSD as539be (2018)

Xtriage (Phenix) : 1.13EDS : trunk31020

Percentile statistics : 20171227.v01 (using entries in the PDB archive December 27th 2017)Refmac : 5.8.0158CCP4 : 7.0 (Gargrove)

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

Validation Pipeline (wwPDB-VP) : trunk31020

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



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

Full wwPDB X-ray Structure Validation Report 1Q84

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 2.45 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.

Metric Whole archive(#Entries)

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

Rfree 111664 1259 (2.48-2.44)Clashscore 122126 1323 (2.48-2.44)

Ramachandran outliers 120053 1314 (2.48-2.44)Sidechain outliers 120020 1314 (2.48-2.44)RSRZ outliers 108989 1238 (2.48-2.44)

The table below summarises the geometric issues observed across the polymeric chains and their fitto the electron density. The red, orange, yellow and green segments on the lower bar indicate thefraction of residues that contain outliers for >=3, 2, 1 and 0 types of geometric quality criteria. Agrey segment represents the fraction of residues that are not modelled. The numeric value for eachfraction 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 theelectron density. The numeric value is given above the bar.

Mol Chain Length Quality of chain

1 A 580

1 B 580

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


2 Entry composition i○

There are 5 unique types of molecules in this entry. The entry contains 8799 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 Acetylcholinesterase.

Mol Chain Residues Atoms ZeroOcc AltConf Trace

1 A 536 Total C N O S4172 2678 723 757 14 0 0 0

1 B 531 Total C N O S4142 2662 715 751 14 0 0 0

• Molecule 2 is N-ACETYL-D-GLUCOSAMINE (three-letter code: NAG) (formula: C8H15NO6).

Mol Chain Residues Atoms ZeroOcc AltConf

2 A 1 Total C N O14 8 1 5 0 0

2 A 1 Total C N O14 8 1 5 0 0

• Molecule 3 is HEXAETHYLENE GLYCOL (three-letter code: P6G) (formula: C12H26O7).

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



3 A 1 Total C O19 12 7 0 0

• Molecule 4 is 3,8-DIAMINO-6-PHENYL-5-[6-[1-[2-[(1,2,3,4-TETRAHYDRO-9-ACRIDINYL)AMINO]ETHYL]-1H-1,2,3-TRIAZOL-4-YL]HEXYL]-PHENANTHRIDINIUM(three-letter code: TZ4) (formula: C42H45N8).


4 A 1 Total C N50 42 8 0 0

4 B 1 Total C N50 42 8 0 0


• Molecule 5 is water.


5 A 214 Total O214 214 0 0

5 B 124 Total O124 124 0 0


3 Residue-property plots i○

These plots are drawn for all protein, RNA and DNA chains in the entry. The first 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 geometryand 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 fit 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: Acetylcholinesterase

Chain A:

MET

ARG

PRO

PRO

TRP

TYR

PRO

LEU

HIS

THR

PRO

SER

LEU

ALA

PHE

PRO

LEU

LEU

PHE

LEU

LEU

LEU

SER

LEU

LEU

GLY

GLY

GLY

ALA

ARG

ALA

E1 G2 R3 E4 R13

R18

K23

R45

Y70

T112

P113

G143

L161

I187

M195

S196

V197

F200

L216

H223

R224

A225

V226

R245

R246

T249

L250

L251

P258

PRO

GLY

GLY

ALA

GLY

G264•

I270

R274

Q291

F295

V300

P301

E313

Q322

D323•

L324

Q325

V326

L327

V328

Y337

D349

L353

R356

Q369

H381

E389

D390

P391

T392

H393

D396

Q413

R424

A427

R433

L437

Y449

P458

Y465

R475

K478

R485

T486

G487

D491

P492

R493•

D494•

S495•

K496•

S497•

W500

L524

R525

A526

Q527

F531

L536

L540•

S541•

ALA

THR

ASP

THR

LEU

ASP

GLU

ALA

• Molecule 1: Acetylcholinesterase

Chain B:

MET

ARG

PRO

PRO

TRP

TYR

PRO

LEU

HIS

THR

PRO

SER

LEU

ALA

PHE

PRO

LEU

LEU

PHE

LEU

LEU

LEU

SER

LEU

LEU

GLY

GLY

GLY

ALA

ARG

ALA

GLU

GLY

ARG

E4 D5 R11

R21

S30

P41•

V42•

D61

D74

T103

A109•

T112

L115

L130

Y133

R136

G143

L161

R165

D193

P194

M195

S196

V197

F200

M211

H223

R245

R246

T249

P258

PRO

GLY

GLY

ALA

GLY

GLY

N265

L269

L281

Q291

I294

F295

D306

F307

L308

D320

V328

Y337

F338

D349

Q369

E389

D390

D396

V402

G403

D404

Q413

R424

A427

W439

P458

P461

Y465

D488

D491

D494

S497

P498

R525

T528

F531

R534

F535

L536

L540•

SER

ALA

THR

ASP

THR

LEU

ASP

GLU

ALA

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


4 Data and refinement statistics i○

Property Value SourceSpace group P 21 21 21 DepositorCell constantsa, b, c, α, β, γ

79.27Å 111.77Å 227.17Å90.00◦ 90.00◦ 90.00◦ Depositor

Resolution (Å) 20.00 – 2.4528.86 – 2.45

DepositorEDS

% Data completeness(in resolution range)

99.7 (20.00-2.45)99.7 (28.86-2.45)

DepositorEDS

Rmerge (Not available) DepositorRsym 0.06 Depositor

< I/σ(I) > 1 4.17 (at 2.45Å) XtriageRefinement program REFMAC 5.1.24 Depositor

R, Rfree0.184 , 0.2140.199 , 0.224

DepositorDCC

Rfree test set 1508 reflections (2.02%) wwPDB-VPWilson B-factor (Å2) 47.0 Xtriage

Anisotropy 0.695 XtriageBulk solvent ksol(e/Å3), Bsol(Å2) 0.30 , 36.8 EDS

L-test for twinning2 < |L| > = 0.51, < L2 > = 0.35 XtriageEstimated twinning fraction No twinning to report. Xtriage

Fo,Fc correlation 0.96 EDSTotal number of atoms 8799 wwPDB-VP

Average B, all atoms (Å2) 54.0 wwPDB-VP

Xtriage’s analysis on translational NCS is as follows: The largest off-origin peak in the Pattersonfunction is 2.72% of the height of the origin peak. No significant pseudotranslation is detected.

1Intensities estimated from amplitudes.2Theoretical values of < |L| >, < L2 > for acentric reflections 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 i○

5.1 Standard geometry i○

Bond lengths and bond angles in the following residue types are not validated in this section:NAG, P6G, TZ4

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 Chain Bond lengths Bond anglesRMSZ #|Z| >5 RMSZ #|Z| >5

1 A 0.72 0/4296 0.88 8/5872 (0.1%)1 B 0.67 0/4266 0.83 13/5833 (0.2%)All All 0.70 0/8562 0.86 21/11705 (0.2%)

Chiral center outliers are detected by calculating the chiral volume of a chiral center and verifying ifthe center is modelled as a planar moiety or with the opposite hand.A planarity outlier is detectedby checking planarity of atoms in a peptide group, atoms in a mainchain group or atoms of asidechain that are expected to be planar.

Mol Chain #Chirality outliers #Planarity outliers1 B 0 1

There are no bond length outliers.

All (21) bond angle outliers are listed below:

Mol Chain Res Type Atoms Z Observed(o) Ideal(o)1 B 404 ASP CB-CG-OD2 6.96 124.56 118.301 A 396 ASP CB-CG-OD2 6.89 124.50 118.301 B 74 ASP CB-CG-OD2 6.87 124.48 118.301 A 491 ASP CB-CG-OD2 6.61 124.25 118.301 A 390 ASP CB-CG-OD2 6.49 124.14 118.301 B 5 ASP CB-CG-OD2 6.13 123.82 118.301 B 349 ASP CB-CG-OD2 6.05 123.75 118.301 B 396 ASP CB-CG-OD2 6.04 123.73 118.301 B 320 ASP CB-CG-OD2 5.97 123.68 118.301 A 433 ARG NE-CZ-NH2 -5.90 117.35 120.301 B 498 PRO N-CA-C -5.74 97.17 112.101 A 433 ARG NE-CZ-NH1 5.55 123.07 120.301 B 488 ASP CB-CG-OD2 5.51 123.26 118.301 A 349 ASP CB-CG-OD2 5.41 123.17 118.30

Continued on next page...

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

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


Continued from previous page...Mol Chain Res Type Atoms Z Observed(o) Ideal(o)1 B 193 ASP CB-CG-OD2 5.39 123.15 118.301 B 491 ASP CB-CG-OD2 5.39 123.15 118.301 B 390 ASP CB-CG-OD2 5.37 123.13 118.301 A 18 ARG NE-CZ-NH2 -5.31 117.64 120.301 A 475 ARG NE-CZ-NH2 -5.25 117.67 120.301 B 306 ASP CB-CG-OD2 5.17 122.95 118.301 B 494 ASP CB-CG-OD2 5.10 122.89 118.30

There are no chirality outliers.

All (1) planarity outliers are listed below:

Mol Chain Res Type Group1 B 497 SER Peptide

5.2 Too-close contacts i○

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 4172 0 4050 27 01 B 4142 0 4023 17 02 A 28 0 26 0 03 A 19 0 26 3 04 A 50 0 45 1 04 B 50 0 45 1 05 A 214 0 0 6 05 B 124 0 0 2 0All All 8799 0 8215 45 0

The all-atom clashscore is defined as the number of clashes found per 1000 atoms (includinghydrogen atoms). The all-atom clashscore for this structure is 3.

All (45) close contacts within the same asymmetric unit are listed below, sorted by their clashmagnitude.

Atom-1 Atom-2 Interatomicdistance (Å)

Clashoverlap (Å)

1:B:197:VAL:H 1:B:223:HIS:HD2 1.36 0.72Continued on next page...

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


Continued from previous page...


Clashoverlap (Å)

1:B:30:SER:HB2 1:B:103:THR:HG22 1.71 0.711:B:245:ARG:O 1:B:249:THR:HG23 1.94 0.67

1:B:112:THR:HG21 1:B:143:GLY:O 1.96 0.654:A:951:TZ4:H291 5:A:1755:HOH:O 1.96 0.651:A:4:GLU:OE2 1:A:18:ARG:HD3 1.99 0.611:A:197:VAL:H 1:A:223:HIS:HD2 1.48 0.61

1:A:527:GLN:HG3 3:A:901:P6G:H22 1.83 0.591:B:534:ARG:HD3 5:B:1075:HOH:O 2.02 0.581:A:325:GLN:HE21 1:A:487:GLY:HA3 1.68 0.581:A:113:PRO:HG2 1:A:485:ARG:HG2 1.86 0.571:A:112:THR:HG21 1:A:143:GLY:O 2.05 0.561:B:211:MET:HG2 1:B:308:LEU:HD21 1.90 0.541:A:369:GLN:HB2 5:A:1726:HOH:O 2.09 0.521:A:13:ARG:NH2 5:A:1722:HOH:O 2.43 0.511:A:245:ARG:O 1:A:249:THR:HG23 2.11 0.501:A:328:VAL:O 1:A:427:ALA:HA 2.12 0.49

1:A:274:ARG:HD3 5:A:1794:HOH:O 2.12 0.481:A:433:ARG:HD3 5:A:1810:HOH:O 2.13 0.481:A:300:VAL:HB 1:A:301:PRO:HD2 1.95 0.48

1:A:161:LEU:HD12 1:A:270:ILE:HD11 1.96 0.481:A:458:PRO:HA 1:A:465:TYR:CD2 2.50 0.471:A:381:HIS:HA 3:A:901:P6G:H172 1.96 0.461:B:328:VAL:O 1:B:427:ALA:HA 2.15 0.461:A:393:HIS:HB2 5:A:1780:HOH:O 2.14 0.461:A:437:LEU:HD11 1:A:449:TYR:CD2 2.50 0.461:B:458:PRO:HA 1:B:465:TYR:CD2 2.51 0.461:B:369:GLN:HB3 5:B:1024:HOH:O 2.16 0.461:A:224:ARG:HD3 1:A:325:GLN:NE2 2.31 0.451:A:353:LEU:HB3 1:A:391:PRO:HB2 1.98 0.441:B:497:SER:HB2 1:B:498:PRO:HA 2.00 0.431:B:528:THR:O 1:B:531:PHE:HB3 2.18 0.431:B:497:SER:CB 1:B:498:PRO:HA 2.49 0.431:A:200:PHE:CB 1:A:226:VAL:HB 2.48 0.431:A:245:ARG:O 1:A:249:THR:CG2 2.67 0.42

1:A:224:ARG:HG2 1:A:325:GLN:HB2 2.01 0.421:B:294:ILE:HD11 1:B:402:VAL:HG21 2.02 0.421:B:130:LEU:HD12 1:B:133:TYR:CE2 2.55 0.421:B:439:TRP:CZ2 4:B:952:TZ4:H36 2.55 0.411:B:161:LEU:HD11 1:B:269:LEU:HD22 2.03 0.411:A:531:PHE:HB2 3:A:901:P6G:H62 2.02 0.411:A:327:LEU:HD11 1:A:500:TRP:CH2 2.56 0.41



Continued from previous page...


Clashoverlap (Å)

1:A:187:ILE:HD12 1:A:187:ILE:HA 1.94 0.411:A:291:GLN:HE22 1:A:369:GLN:NE2 2.19 0.401:B:295:PHE:CE2 1:B:338:PHE:CE1 3.09 0.40

There are no symmetry-related clashes.

5.3 Torsion angles i○

5.3.1 Protein backbone i○

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 532/580 (92%) 517 (97%) 15 (3%) 0 100 100

1 B 527/580 (91%) 511 (97%) 15 (3%) 1 (0%) 49 59

All All 1059/1160 (91%) 1028 (97%) 30 (3%) 1 (0%) 53 66

All (1) Ramachandran outliers are listed below:

Mol Chain Res Type1 B 497 SER

5.3.2 Protein sidechains i○

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 437/473 (92%) 408 (93%) 29 (7%) 18 23

1 B 435/473 (92%) 414 (95%) 21 (5%) 28 37Continued on next page...

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

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

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


Continued from previous page...Mol Chain Analysed Rotameric Outliers Percentiles

All All 872/946 (92%) 822 (94%) 50 (6%) 23 29

All (50) residues with a non-rotameric sidechain are listed below:

Mol Chain Res Type1 A 3 ARG1 A 4 GLU1 A 13 ARG1 A 23 LYS1 A 45 ARG1 A 70 TYR1 A 195 MET1 A 200 PHE1 A 216 LEU1 A 246 ARG1 A 249 THR1 A 251 LEU1 A 291 GLN1 A 295 PHE1 A 313 GLU1 A 322 GLN1 A 325 GLN1 A 337 TYR1 A 356 ARG1 A 389 GLU1 A 413 GLN1 A 424 ARG1 A 433 ARG1 A 478 LYS1 A 497 SER1 A 524 LEU1 A 525 ARG1 A 536 LEU1 A 540 LEU1 B 11 ARG1 B 21 ARG1 B 61 ASP1 B 115 LEU1 B 136 ARG1 B 165 ARG1 B 195 MET1 B 200 PHE



Continued from previous page...Mol Chain Res Type1 B 246 ARG1 B 249 THR1 B 281 LEU1 B 291 GLN1 B 295 PHE1 B 337 TYR1 B 369 GLN1 B 389 GLU1 B 413 GLN1 B 424 ARG1 B 461 PRO1 B 525 ARG1 B 536 LEU

Some sidechains can be flipped to improve hydrogen bonding and reduce clashes. All (6) suchsidechains are listed below:

Mol Chain Res Type1 A 223 HIS1 A 291 GLN1 A 325 GLN1 B 223 HIS1 B 291 GLN1 B 369 GLN

5.3.3 RNA i○

There are no RNA molecules in this entry.

5.4 Non-standard residues in protein, DNA, RNA chains i○

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

5.5 Carbohydrates i○

There are no carbohydrates in this entry.

5.6 Ligand geometry i○

5 ligands are modelled in this entry.

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

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




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 defined 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 Link Bond lengths Bond anglesCounts RMSZ #|Z| > 2 Counts RMSZ #|Z| > 2

2 NAG A 1501 1 14,14,15 1.18 1 (7%) 17,19,21 1.95 3 (17%)2 NAG A 1701 1 14,14,15 0.76 0 17,19,21 1.73 5 (29%)3 P6G A 901 - 18,18,18 2.06 6 (33%) 17,17,17 1.28 1 (5%)4 TZ4 A 951 - 56,57,57 1.54 8 (14%) 66,80,80 2.15 18 (27%)4 TZ4 B 952 - 56,57,57 1.68 11 (19%) 66,80,80 2.34 21 (31%)

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 defined in theChemical Component Dictionary. Similar counts are reported in the Torsion and Rings columns.’-’ means no outliers of that kind were identified.

Mol Type Chain Res Link Chirals Torsions Rings2 NAG A 1501 1 - 0/6/23/26 0/1/1/12 NAG A 1701 1 - 0/6/23/26 0/1/1/13 P6G A 901 - - 0/16/16/16 0/0/0/04 TZ4 A 951 - - 0/19/26/26 0/8/8/84 TZ4 B 952 - - 1/19/26/26 0/8/8/8

All (26) bond length outliers are listed below:

Mol Chain Res Type Atoms Z Observed(Å) Ideal(Å)4 B 952 TZ4 C40-C39 -5.21 1.43 1.514 A 951 TZ4 C40-C39 -4.46 1.44 1.514 B 952 TZ4 C38-C37 -4.00 1.45 1.504 B 952 TZ4 C41-C40 -3.87 1.37 1.514 B 952 TZ4 C42-C38 -3.83 1.37 1.514 A 951 TZ4 C41-C40 -3.81 1.37 1.514 A 951 TZ4 C38-C37 -3.65 1.45 1.504 A 951 TZ4 C42-C38 -3.63 1.38 1.514 B 952 TZ4 C42-C41 -2.27 1.42 1.514 A 951 TZ4 C42-C41 -2.20 1.42 1.514 A 951 TZ4 C27-N6 -2.19 1.33 1.354 A 951 TZ4 C3-C4 2.14 1.45 1.41



Continued from previous page...Mol Chain Res Type Atoms Z Observed(Å) Ideal(Å)4 B 952 TZ4 C6-N2 2.23 1.43 1.404 B 952 TZ4 C14-C16 2.23 1.45 1.424 B 952 TZ4 C37-N8 2.32 1.35 1.324 B 952 TZ4 C15-C14 2.41 1.46 1.424 B 952 TZ4 C30-C39 2.64 1.43 1.393 A 901 P6G O7-C6 2.74 1.54 1.424 B 952 TZ4 C39-C37 2.87 1.44 1.404 A 951 TZ4 C39-C37 2.93 1.44 1.403 A 901 P6G O4-C3 3.24 1.56 1.423 A 901 P6G O19-C18 3.24 1.59 1.423 A 901 P6G O16-C15 3.40 1.57 1.422 A 1501 NAG C1-C2 3.51 1.57 1.523 A 901 P6G O13-C12 3.67 1.58 1.423 A 901 P6G O10-C9 3.90 1.59 1.42

All (48) bond angle outliers are listed below:

Mol Chain Res Type Atoms Z Observed(o) Ideal(o)4 B 952 TZ4 C40-C39-C37 -9.68 112.36 121.114 A 951 TZ4 C40-C39-C37 -7.49 114.34 121.114 A 951 TZ4 C28-N6-C27 -3.92 120.61 129.824 B 952 TZ4 C28-C29-N7 -3.87 103.97 112.524 A 951 TZ4 C9-C8-C7 -3.57 114.82 120.214 B 952 TZ4 C9-C8-C7 -3.36 115.14 120.214 B 952 TZ4 C28-N6-C27 -3.06 122.62 129.824 A 951 TZ4 C24-C25-C26 -3.05 102.67 113.172 A 1701 NAG C3-C4-C5 -2.93 105.01 110.244 B 952 TZ4 C17-C16-C14 -2.87 114.10 117.744 A 951 TZ4 C17-C16-C14 -2.85 114.12 117.744 A 951 TZ4 C28-C29-N7 -2.58 106.82 112.524 B 952 TZ4 C24-C25-C26 -2.40 104.92 113.174 A 951 TZ4 C18-C19-C15 -2.38 114.66 119.684 A 951 TZ4 C29-C28-N6 -2.36 106.95 110.924 A 951 TZ4 C38-C37-C39 -2.21 119.32 121.504 B 952 TZ4 C18-C19-C15 -2.19 115.06 119.684 B 952 TZ4 C2-C1-C5 -2.17 115.11 119.684 A 951 TZ4 C2-C1-C5 -2.11 115.23 119.682 A 1501 NAG O7-C7-C8 -2.09 118.29 122.074 B 952 TZ4 C8-C7-C14 -2.08 116.94 121.364 B 952 TZ4 C3-C4-C6 -2.03 114.87 117.784 B 952 TZ4 C32-C31-C33 -2.02 116.26 118.352 A 1701 NAG O5-C5-C4 -2.02 105.92 110.83



Continued from previous page...Mol Chain Res Type Atoms Z Observed(o) Ideal(o)4 B 952 TZ4 C36-C32-C31 2.01 123.65 120.892 A 1701 NAG C6-C5-C4 2.04 117.80 112.994 A 951 TZ4 C35-C34-C33 2.12 123.21 120.084 B 952 TZ4 C42-C41-C40 2.15 121.87 112.504 B 952 TZ4 C8-C7-N2 2.24 123.14 120.464 A 951 TZ4 C37-N8-C33 2.40 120.50 117.714 B 952 TZ4 C2-C3-C4 2.44 124.99 121.572 A 1701 NAG O4-C4-C5 2.55 115.70 109.313 A 901 P6G O1-C2-C3 3.13 130.28 111.914 B 952 TZ4 C19-C15-C14 3.53 124.18 120.814 B 952 TZ4 C13-C8-C7 3.54 125.56 120.212 A 1701 NAG O5-C5-C6 3.72 113.03 107.154 A 951 TZ4 C42-C38-C37 3.72 119.84 113.554 A 951 TZ4 N4-N5-N6 3.95 110.29 107.312 A 1501 NAG O5-C5-C6 4.13 113.69 107.154 A 951 TZ4 C19-C15-C14 4.30 124.91 120.814 A 951 TZ4 C41-C40-C39 4.43 121.90 112.854 A 951 TZ4 C39-C30-N7 4.72 128.62 119.544 A 951 TZ4 C13-C8-C7 4.81 127.49 120.212 A 1501 NAG C1-O5-C5 4.83 118.84 112.194 B 952 TZ4 N4-N5-N6 4.87 110.99 107.314 B 952 TZ4 C42-C38-C37 5.27 122.47 113.554 B 952 TZ4 C41-C40-C39 5.36 123.82 112.854 B 952 TZ4 C39-C30-N7 5.65 130.41 119.54

There are no chirality outliers.

All (1) torsion outliers are listed below:

Mol Chain Res Type Atoms4 B 952 TZ4 C29-C28-N6-N5

There are no ring outliers.

3 monomers are involved in 5 short contacts:

Mol Chain Res Type Clashes Symm-Clashes3 A 901 P6G 3 04 A 951 TZ4 1 04 B 952 TZ4 1 0


5.7 Other polymers i○

There are no such residues in this entry.

5.8 Polymer linkage issues i○

There are no chain breaks in this entry.


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


6 Fit of model and data i○

6.1 Protein, DNA and RNA chains i○

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 536/580 (92%) -0.34 9 (1%) 70 66 36, 50, 72, 99 0

1 B 531/580 (91%) -0.16 4 (0%) 86 86 39, 55, 77, 97 0

All All 1067/1160 (91%) -0.25 13 (1%) 79 77 36, 52, 75, 99 0

All (13) RSRZ outliers are listed below:

Mol Chain Res Type RSRZ1 A 540 LEU 6.91 A 495 SER 3.71 A 497 SER 3.61 A 264 GLY 3.41 A 541 SER 3.11 B 41 PRO 3.01 A 494 ASP 3.01 B 42 VAL 2.61 A 493 ARG 2.61 B 109 ALA 2.51 A 496 LYS 2.31 A 323 ASP 2.21 B 540 LEU 2.1

6.2 Non-standard residues in protein, DNA, RNA chains i○

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

6.3 Carbohydrates i○

There are no carbohydrates in this entry.

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

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

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



6.4 Ligands i○

In the following table, the Atoms column lists the number of modelled atoms in the group and thenumber defined 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 NAG A 1701 14/15 0.81 0.42 86,95,98,99 04 TZ4 B 952 50/50 0.86 0.19 53,71,77,78 02 NAG A 1501 14/15 0.86 0.39 79,87,94,94 03 P6G A 901 19/19 0.90 0.19 61,72,83,86 04 TZ4 A 951 50/50 0.90 0.16 44,62,66,67 0

6.5 Other polymers i○

There are no such residues in this entry.



full wwpdb x-ray structure validation report...

Documents