Full wwPDB X-ray Structure Validation Report i○

Mar 9, 2018 – 07:45 am GMT

PDB ID : 1NUHTitle : The crystal structure of human phosphoglucose isomerase complexed with 5-

phosphoarabinonateAuthors : Davies, C.

Deposited on : 2003-01-31Resolution : 2.51 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.orgA 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 : trunk30967

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) : trunk30967

Page 2 Full wwPDB X-ray Structure Validation Report 1NUH

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 2.51 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 4155 (2.50-2.50)Clashscore 122126 4827 (2.50-2.50)

Ramachandran outliers 120053 4735 (2.50-2.50)Sidechain outliers 120020 4737 (2.50-2.50)RSRZ outliers 108989 4058 (2.50-2.50)

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 558

Page 3 Full wwPDB X-ray Structure Validation Report 1NUH

2 Entry composition i○

There are 4 unique types of molecules in this entry. The entry contains 4578 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 glucose phosphate isomerase.

Mol Chain Residues Atoms ZeroOcc AltConf Trace

1 A 555 Total C N O S4424 2819 778 809 18 0 0 0

• Molecule 2 is SULFATE ION (three-letter code: SO4) (formula: O4S).

Mol Chain Residues Atoms ZeroOcc AltConf

2 A 1 Total O S5 4 1 0 0

2 A 1 Total O S5 4 1 0 0

2 A 1 Total O S5 4 1 0 0

2 A 1 Total O S5 4 1 0 0

2 A 1 Total O S5 4 1 0 0

Continued on next page...

Page 4 Full wwPDB X-ray Structure Validation Report 1NUH

Continued from previous page...Mol Chain Residues Atoms ZeroOcc AltConf

2 A 1 Total O S5 4 1 0 0

• Molecule 3 is 5-PHOSPHOARABINONIC ACID (three-letter code: PA5) (formula: C5H11O9P).

Mol Chain Residues Atoms ZeroOcc AltConf

3 A 1 Total C O P15 5 9 1 0 0

• Molecule 4 is water.

Mol Chain Residues Atoms ZeroOcc AltConf

4 A 109 Total O109 109 0 0

Page 5 Full wwPDB X-ray Structure Validation Report 1NUH

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: glucose phosphate isomerase

Chain A:

MET

A1 T4 R5•

D6 P7 Q8•

F9 Q10•

K11

L12•

Q13

Q14•

R17

E18•

H19•

R20

S21

E22

L23•

L28•

F29•

D30•

A31

N32•

K33•

D34•

R35

L41

T42

L43

N44

T45

N46

D53

R65

R74

E77

R80

F84

L98

L102

R103

D116

P119

L125

D126

K127

Q133•

R136

S137

G138•

D139•

W140

K141

D150

V151

I152

G155

D160

L164

A169

L170

K171

P172

P178

R179

V180

V183

S184

N185

I186

I191

A192

K193

T194

L195

I206

F212

E216

N220

K225

E226

W227

F228

L229

Q230

A231•

A239

L245

T249

T250

K251

V252

K253

E254

F255

G256

I257•

D258•

M262

W268

V269•

I279

G280

L281

S282

I283

H286

V287

D290•

L296

F306

R307

E312

K313

N314

A315

P316

I324

W325

N328

C329

F330

G331

C332

H335

A336•

P339

Y343

L344

H345

R346

F347•

Q353

G354

D355

M356

E357

S366

G367

T368

D371

V378•

W379•

P382

Q387

F390•

Y391

I394

M400

D404

F405

L406

I407

P408

N427

F428

L435

M436

R437•

G438•

K446

A451•

E456•

D457

R460•

L461

L462

P463

R471

T482

P483

V490•

E494

W504

D505

I506

N507

D510

E515

K518

Q519•

K523

I524

E525

P526

G530

S531•

V534•

H537

T541

N542•

I545

R552

E553•

A554•

R555

VAL

GLN

Page 6 Full wwPDB X-ray Structure Validation Report 1NUH

4 Data and refinement statistics i○

Property Value SourceSpace group P 43 21 2 DepositorCell constantsa, b, c, α, β, γ

94.40Å 94.40Å 137.10Å90.00◦ 90.00◦ 90.00◦ Depositor

Resolution (Å) 50.00 – 2.5147.82 – 2.51

DepositorEDS

% Data completeness(in resolution range)

98.4 (50.00-2.51)97.7 (47.82-2.51)

DepositorEDS

Rmerge 0.13 DepositorRsym 0.13 Depositor

< I/σ(I) > 1 2.72 (at 2.51Å) XtriageRefinement program REFMAC 5.0 Depositor

R, Rfree0.214 , 0.2680.243 , 0.281

DepositorDCC

Rfree test set 1101 reflections (5.13%) wwPDB-VPWilson B-factor (Å2) 27.3 Xtriage

Anisotropy 0.212 XtriageBulk solvent ksol(e/Å3), Bsol(Å2) 0.37 , 38.5 EDS

L-test for twinning2 < |L| > = 0.52, < L2 > = 0.35 XtriageEstimated twinning fraction No twinning to report. Xtriage

Fo,Fc correlation 0.89 EDSTotal number of atoms 4578 wwPDB-VP

Average B, all atoms (Å2) 25.0 wwPDB-VP

Xtriage’s analysis on translational NCS is as follows: The largest off-origin peak in the Pattersonfunction is 5.54% 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.

Page 7 Full wwPDB X-ray Structure Validation Report 1NUH

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: SO4,PA5

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 0.55 0/4532 0.82 11/6137 (0.2%)

There are no bond length outliers.

All (11) bond angle outliers are listed below:

Mol Chain Res Type Atoms Z Observed(o) Ideal(o)1 A 505 ASP CB-CG-OD2 7.10 124.69 118.301 A 150 ASP CB-CG-OD2 6.76 124.38 118.301 A 371 ASP CB-CG-OD2 6.72 124.35 118.301 A 404 ASP CB-CG-OD2 6.14 123.83 118.301 A 290 ASP CB-CG-OD2 5.84 123.55 118.301 A 139 ASP CB-CG-OD2 5.68 123.41 118.301 A 53 ASP CB-CG-OD2 5.59 123.34 118.301 A 126 ASP CB-CG-OD2 5.58 123.33 118.301 A 457 ASP CB-CG-OD2 5.47 123.22 118.301 A 355 ASP CB-CG-OD2 5.31 123.08 118.301 A 510 ASP CB-CG-OD2 5.22 123.00 118.30

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 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.

Page 8 Full wwPDB X-ray Structure Validation Report 1NUH

Mol Chain Non-H H(model) H(added) Clashes Symm-Clashes1 A 4424 0 4375 90 02 A 30 0 0 2 03 A 15 0 8 0 04 A 109 0 0 7 1All All 4578 0 4383 90 1

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 10.

All (90) close contacts within the same asymmetric unit are listed below, sorted by their clashmagnitude.

Atom-1 Atom-2 Interatomicdistance (Å)

Clashoverlap (Å)

1:A:366:SER:OG 1:A:368:THR:HG23 1.68 0.941:A:14:GLN:HE22 1:A:17:ARG:NH1 1.78 0.811:A:6:ASP:OD1 4:A:609:HOH:O 1.99 0.801:A:523:LYS:O 1:A:526:PRO:HD2 1.84 0.771:A:530:GLY:O 1:A:552:ARG:NH2 2.18 0.771:A:77:GLU:HG3 4:A:615:HOH:O 1.83 0.77

1:A:249:THR:HG22 1:A:253:LYS:HE3 1.68 0.751:A:136:ARG:NE 2:A:560:SO4:O1 2.18 0.691:A:324:ILE:HG23 1:A:328:ASN:HD22 1.56 0.691:A:328:ASN:HD21 1:A:504:TRP:HE1 1.37 0.691:A:35:ARG:HD2 4:A:637:HOH:O 1.91 0.681:A:330:PHE:HB3 1:A:400:MET:CE 2.24 0.671:A:14:GLN:NE2 1:A:17:ARG:HH11 1.94 0.661:A:330:PHE:HB3 1:A:400:MET:HE3 1.78 0.661:A:391:TYR:HA 1:A:394:ILE:HD12 1.78 0.661:A:315:ALA:HB3 1:A:316:PRO:HD3 1.78 0.651:A:366:SER:OG 1:A:368:THR:CG2 2.45 0.641:A:283:ILE:O 1:A:287:VAL:HG22 1.98 0.62

1:A:29:PHE:CE2 1:A:35:ARG:HG2 2.36 0.611:A:387:GLN:HE22 1:A:427:ASN:HB3 1.66 0.601:A:14:GLN:CD 1:A:17:ARG:HH11 2.04 0.601:A:332:CYS:SG 1:A:400:MET:HE2 2.41 0.601:A:332:CYS:SG 1:A:400:MET:CE 2.90 0.601:A:33:LYS:H 1:A:33:LYS:HD3 1.67 0.59

1:A:314:ASN:OD1 1:A:316:PRO:HD2 2.03 0.581:A:74:ARG:HD2 4:A:609:HOH:O 2.02 0.581:A:14:GLN:NE2 1:A:17:ARG:NH1 2.47 0.581:A:45:THR:O 1:A:46:ASN:HB2 2.03 0.58

1:A:518:LYS:HG2 4:A:648:HOH:O 2.04 0.571:A:225:LYS:NZ 1:A:255:PHE:O 2.38 0.56

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Page 9 Full wwPDB X-ray Structure Validation Report 1NUH

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Atom-1 Atom-2 Interatomicdistance (Å)

Clashoverlap (Å)

1:A:541:THR:O 1:A:545:ILE:HG13 2.06 0.561:A:482:THR:HB 1:A:483:PRO:HD2 1.90 0.541:A:19:HIS:O 1:A:20:ARG:C 2.47 0.53

1:A:183:VAL:HG12 1:A:220:ASN:ND2 2.24 0.531:A:324:ILE:HG23 1:A:328:ASN:ND2 2.24 0.521:A:330:PHE:CD1 1:A:400:MET:HE1 2.45 0.521:A:312:GLU:CD 1:A:312:GLU:H 2.13 0.511:A:353:GLN:O 1:A:357:GLU:HB3 2.11 0.50

1:A:462:LEU:HB3 1:A:463:PRO:HD3 1.93 0.501:A:245:LEU:HD13 1:A:279:ILE:HA 1.94 0.491:A:325:TRP:O 1:A:329:CYS:HB2 2.13 0.481:A:171:LYS:N 1:A:172:PRO:CD 2.76 0.481:A:186:ILE:HB 1:A:216:GLU:CG 2.44 0.471:A:537:HIS:HB2 1:A:542:ASN:OD1 2.15 0.461:A:102:LEU:HD11 1:A:269:VAL:HG22 1.98 0.461:A:191:ILE:HG23 1:A:192:ALA:N 2.30 0.461:A:206:ILE:HD13 1:A:281:LEU:HD23 1.98 0.461:A:171:LYS:HE3 1:A:286:HIS:HE1 1.81 0.461:A:332:CYS:SG 1:A:400:MET:HE3 2.56 0.461:A:490:VAL:O 1:A:494:GLU:HG3 2.16 0.46

1:A:400:MET:HB3 1:A:400:MET:HE2 1.79 0.451:A:103:ARG:CB 1:A:296:LEU:HB3 2.47 0.451:A:169:ALA:HA 1:A:343:TYR:HB3 1.99 0.451:A:394:ILE:O 1:A:471:ARG:NE 2.49 0.45

1:A:435:LEU:HD23 1:A:435:LEU:HA 1.80 0.441:A:103:ARG:HB2 1:A:296:LEU:HB3 1.99 0.441:A:152:ILE:N 1:A:152:ILE:HD12 2.32 0.441:A:141:LYS:O 2:A:561:SO4:O2 2.35 0.44

1:A:133:GLN:HB3 1:A:133:GLN:HE21 1.63 0.441:A:345:HIS:HA 1:A:382:PRO:HG3 2.00 0.44

1:A:164:LEU:HD23 1:A:164:LEU:C 2.38 0.431:A:98:LEU:HB2 1:A:268:TRP:CE3 2.53 0.431:A:229:LEU:HA 1:A:229:LEU:HD23 1.85 0.431:A:178:PRO:O 1:A:286:HIS:HD2 2.01 0.431:A:74:ARG:NH1 1:A:505:ASP:HB2 2.34 0.431:A:330:PHE:CB 1:A:400:MET:HE3 2.46 0.421:A:255:PHE:HD1 1:A:257:ILE:HG13 1.84 0.421:A:127:LYS:HE2 1:A:262:MET:O 2.19 0.421:A:446:LYS:HB3 1:A:446:LYS:HE2 1.87 0.421:A:138:GLY:O 1:A:141:LYS:HE2 2.19 0.421:A:155:GLY:O 1:A:160:ASP:HB2 2.19 0.42

Continued on next page...

Page 10 Full wwPDB X-ray Structure Validation Report 1NUH

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Atom-1 Atom-2 Interatomicdistance (Å)

Clashoverlap (Å)

1:A:339:PRO:O 1:A:382:PRO:HA 2.19 0.421:A:84:PHE:HB3 1:A:307:ARG:CZ 2.49 0.421:A:405:PHE:HB3 1:A:428:PHE:CE1 2.55 0.411:A:250:THR:O 1:A:254:GLU:HG3 2.21 0.411:A:33:LYS:H 1:A:33:LYS:CD 2.27 0.41

1:A:407:ILE:HG13 1:A:408:PRO:HD2 2.02 0.411:A:239:ALA:HA 4:A:634:HOH:O 2.20 0.411:A:335:HIS:O 1:A:378:VAL:HA 2.20 0.41

1:A:125:LEU:HD23 1:A:125:LEU:HA 1.90 0.411:A:191:ILE:CG2 1:A:192:ALA:N 2.82 0.411:A:356:MET:HA 4:A:588:HOH:O 2.20 0.411:A:80:ARG:HG3 1:A:306:PHE:CE2 2.56 0.411:A:116:ASP:O 1:A:119:PRO:HD2 2.21 0.411:A:19:HIS:O 1:A:21:SER:N 2.54 0.41

1:A:212:PHE:HB3 1:A:251:LYS:HB3 2.03 0.401:A:387:GLN:HG2 1:A:391:TYR:CE2 2.56 0.401:A:195:LEU:HD13 1:A:227:TRP:CG 2.57 0.401:A:482:THR:HB 1:A:483:PRO:CD 2.51 0.401:A:524:ILE:HG12 1:A:524:ILE:H 1.55 0.40

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.

Atom-1 Atom-2 Interatomicdistance (Å)

Clashoverlap (Å)

4:A:567:HOH:O 4:A:567:HOH:O[7_555] 1.39 0.81

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 553/558 (99%) 530 (96%) 23 (4%) 0 100 100

Page 11 Full wwPDB X-ray Structure Validation Report 1NUH

There are no Ramachandran outliers to report.

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 473/477 (99%) 451 (95%) 22 (5%) 29 52

All (22) residues with a non-rotameric sidechain are listed below:

Mol Chain Res Type1 A 4 THR1 A 6 ASP1 A 30 ASP1 A 33 LYS1 A 34 ASP1 A 35 ARG1 A 41 LEU1 A 43 LEU1 A 65 ARG1 A 103 ARG1 A 133 GLN1 A 180 VAL1 A 184 SER1 A 191 ILE1 A 193 LYS1 A 212 PHE1 A 282 SER1 A 368 THR1 A 507 ASN1 A 515 GLU1 A 518 LYS1 A 523 LYS

Some sidechains can be flipped to improve hydrogen bonding and reduce clashes. All (17) suchsidechains are listed below:

Page 12 Full wwPDB X-ray Structure Validation Report 1NUH

Mol Chain Res Type1 A 19 HIS1 A 57 ASN1 A 107 ASN1 A 122 ASN1 A 133 GLN1 A 286 HIS1 A 291 ASN1 A 294 GLN1 A 328 ASN1 A 335 HIS1 A 353 GLN1 A 359 ASN1 A 387 GLN1 A 427 ASN1 A 474 ASN1 A 500 GLN1 A 507 ASN

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○

7 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 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).

Page 13 Full wwPDB X-ray Structure Validation Report 1NUH

Mol Type Chain Res Link Bond lengths Bond anglesCounts RMSZ #|Z| > 2 Counts RMSZ #|Z| > 2

2 SO4 A 558 - 4,4,4 0.14 0 6,6,6 0.32 02 SO4 A 559 - 4,4,4 0.28 0 6,6,6 0.17 02 SO4 A 560 - 4,4,4 0.27 0 6,6,6 0.34 02 SO4 A 561 1 4,4,4 0.13 0 6,6,6 0.18 02 SO4 A 562 - 4,4,4 0.29 0 6,6,6 0.35 02 SO4 A 563 - 4,4,4 0.17 0 6,6,6 0.24 03 PA5 A 564 - 11,14,14 0.81 0 14,20,20 0.77 0

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 SO4 A 558 - - 0/0/0/0 0/0/0/02 SO4 A 559 - - 0/0/0/0 0/0/0/02 SO4 A 560 - - 0/0/0/0 0/0/0/02 SO4 A 561 1 - 0/0/0/0 0/0/0/02 SO4 A 562 - - 0/0/0/0 0/0/0/02 SO4 A 563 - - 0/0/0/0 0/0/0/03 PA5 A 564 - - 0/14/18/18 0/0/0/0

There are no bond length outliers.

There are no bond angle outliers.

There are no chirality outliers.

There are no torsion outliers.

There are no ring outliers.

2 monomers are involved in 2 short contacts:

Mol Chain Res Type Clashes Symm-Clashes2 A 560 SO4 1 02 A 561 SO4 1 0

5.7 Other polymers i○

There are no such residues in this entry.

Page 14 Full wwPDB X-ray Structure Validation Report 1NUH

5.8 Polymer linkage issues i○

There are no chain breaks in this entry.

Page 15 Full wwPDB X-ray Structure Validation Report 1NUH

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 555/558 (99%) 0.75 39 (7%) 16 17 15, 23, 39, 47 0

All (39) RSRZ outliers are listed below:

Mol Chain Res Type RSRZ1 A 32 ASN 5.61 A 30 ASP 4.11 A 19 HIS 3.81 A 10 GLN 3.51 A 553 GLU 3.51 A 531 SER 3.31 A 451 ALA 3.21 A 18 GLU 3.21 A 519 GLN 3.01 A 554 ALA 3.01 A 379 TRP 2.91 A 456 GLU 2.81 A 336 ALA 2.81 A 269 VAL 2.81 A 460 ARG 2.81 A 133 GLN 2.71 A 138 GLY 2.71 A 534 VAL 2.61 A 33 LYS 2.61 A 23 LEU 2.61 A 378 VAL 2.41 A 347 PHE 2.41 A 8 GLN 2.41 A 438 GLY 2.41 A 490 VAL 2.31 A 257 ILE 2.31 A 231 ALA 2.2

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Page 16 Full wwPDB X-ray Structure Validation Report 1NUH

Continued from previous page...Mol Chain Res Type RSRZ1 A 12 LEU 2.21 A 28 LEU 2.21 A 34 ASP 2.21 A 29 PHE 2.21 A 14 GLN 2.21 A 542 ASN 2.21 A 390 PHE 2.11 A 5 ARG 2.11 A 437 ARG 2.11 A 258 ASP 2.01 A 290 ASP 2.01 A 139 ASP 2.0

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.

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 SO4 A 560 5/5 0.82 0.53 53,54,55,55 02 SO4 A 562 5/5 0.83 0.34 53,53,54,54 02 SO4 A 559 5/5 0.85 0.37 55,56,57,57 02 SO4 A 558 5/5 0.89 0.30 48,48,50,51 02 SO4 A 561 5/5 0.91 0.40 60,60,60,61 03 PA5 A 564 15/15 0.93 0.19 21,27,30,31 02 SO4 A 563 5/5 0.93 0.37 58,58,58,59 0

6.5 Other polymers i○

There are no such residues in this entry.