full wwpdb x-ray structure validation report o i · 2020. 8. 8. · rst graphic for a chain...

Full wwPDB X-ray Structure Validation Report iO

Aug 8, 2020 � 11:18 AM BST

PDB ID : 6VT1Title : Naegleria gruberi RNA ligase D172A mutant apo

Authors : Unciuleac, M.C.; Goldgur, Y.; Shuman, S.Deposited on : 2020-02-12Resolution : 2.38 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]

A user guide is available athttps://www.wwpdb.org/validation/2017/XrayValidationReportHelp

with 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 : 2.13.1

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) : 2.13.1

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



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

Full wwPDB X-ray Structure Validation Report 6VT1

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 2.38 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 5509 (2.40-2.36)Clashscore 141614 6082 (2.40-2.36)

Ramachandran outliers 138981 5973 (2.40-2.36)Sidechain outliers 138945 5975 (2.40-2.36)RSRZ outliers 127900 5397 (2.40-2.36)

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 340

1 B 340

1 C 340

1 D 340

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 11143 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 RNA Ligase.

Mol Chain Residues Atoms ZeroOcc AltConf Trace

1 A 339Total C N O S2708 1706 479 513 10

0 0 0

1 B 339Total C N O S2708 1706 479 513 10

0 0 0

1 C 339Total C N O S2708 1706 479 513 10

0 0 0

1 D 339Total C N O S2708 1706 479 513 10

0 0 0

There are 8 discrepancies between the modelled and reference sequences:

Chain Residue Modelled Actual Comment ReferenceA 0 SER - expression tag UNP D2W2Z5A 172 ALA ASP engineered mutation UNP D2W2Z5B 0 SER - expression tag UNP D2W2Z5B 172 ALA ASP engineered mutation UNP D2W2Z5C 0 SER - expression tag UNP D2W2Z5C 172 ALA ASP engineered mutation UNP D2W2Z5D 0 SER - expression tag UNP D2W2Z5D 172 ALA ASP engineered mutation UNP D2W2Z5

� Molecule 2 is ADENOSINEMONOPHOSPHATE (three-letter code: AMP) (formula: C10H14N5O7P)(labeled as "Ligand of Interest" by author).

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


Mol Chain Residues Atoms ZeroOcc AltConf

2 A 1Total C N O P22 10 5 6 1

0 0

2 B 1Total C N O P22 10 5 6 1

0 0

2 C 1Total C N O P22 10 5 6 1

0 0

2 D 1Total C N O P22 10 5 6 1

0 0

� Molecule 3 is water.

Mol Chain Residues Atoms ZeroOcc AltConf

3 A 73Total O73 73

0 0

3 B 48Total O48 48

0 0

3 C 45Total O45 45

0 0

3 D 57Total O57 57

0 0


3 Residue-property plots iO

These plots are drawn for all protein, RNA, DNA and oligosaccharide chains in the entry. The�rst graphic for a chain summarises the proportions of the various outlier classes displayed in thesecond graphic. The second graphic shows the sequence view annotated by issues in geometry andelectron density. Residues are color-coded according to the number of geometric quality criteriafor 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 �t to the electron density (RSRZ > 2). Stretches of 2or more consecutive residues without any outlier are shown as a green connector. Residues presentin the sample, but not in the model, are shown in grey.

• Molecule 1: RNA Ligase

Chain A:

SER

M1•

G2

V3

C26

T33

C34

V35

E40

E58

S67

R77

R80

L81

R82

R85

S91

R100

E103

E115

I116

I126•

S127•

L130•

S131•

G132

E133

I134

P139

I142

D146

Q147

E148

I157

E158

K164

T168

S174

S175

I185

R190

R195

A198•

A201

R208

N209

I212

F217

L224

S232

E238

K239•

L240

K241

I250

Y251

D252

K255

T260

P261

I262

E263

R264

V268

K269

T277

D285

D301

G302

P303

S304

K307

R311

E312

G313

L314

K326

H336

K337

D338•

R339•


Chain B:

SER

M1•

G2•

A21•

E22•

E25

K37

K38

R46•

D59

S67

V70

R80

R85

L86•

M98

D99

Q108•

E115

W122

I126•

S127•

T128•

N129•

L130

E133

I134

L135

G136•

Q147

K161

F165•

V169

A172

W192

E193

L194

R195•

E196

T197

A198•

T199

N200

W203

H204

R208•

N209

L237

E238

K239

L240•

T260

P261

I262

E263

N272

T277

V278

V281

L287

N290•

P303•

S304

L305

N306

K307

N308•

V309

K310

R311

L319

K326

R339


Chain C:

SER

M1•

G2•

V3•

R4

K5

L6

I9

E22

C26

T33

C34

V35

E40

F41

K42

E58

R62

D72

Y73

R77

R80

L81

R82

R85

L90

S91

R100

E103

L104

V109

E115

I116

L117

P124

P125

I126

S127•

T128•

N129

L130•

S131•

G132

E133

P139

T140

F141•

I142

S143

K144

T145

D146

Q147

K161

G162

Q163

K164

S174

S175

M176

T177

V178•

Y179•

R180

D183•

H184

I185

G186

V187•

R190

N191

W192•

R195•

E196•

T197

A198•

T199

N200

W203•

H204

R207

R208

N209

K210

M211•

I212•

E213•

G214

L215

L218•

N221

L222

A223

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


L224•

Q225

I228

E231

N236

L237•

E238

D244

L247

F248

D249

I250•

Y251

D254

K255

A256

Q257

Y258

L259

T260

P261

I262

E263

R264

Q265

S266

L267

V268

K269

Q270

L271•

N272

G275

V278•

K279

D285

P303

S304

L305•

N306

V309

K310

R311

V315

L319•

K326

H336

K337

D338

R339•


Chain D:

SER

M1

G2•

V3

R4

K5

T33

K37

S67

K68

R80

L81

R82

R85

L90

D99

R100

F101•

L104

A105

S106

N107

Q108•

L117

W122

S127

L130•

E133

I134

L135

P139

T140

F141

T145

S175

D183

H184

I185

G186

V187

C188

G189

R190

E193

L194

R195•

A198•

T199•

N200

A201

Q202

W203

H204•

A205

R208

N209

K210

M211

I212

E213•

Q216

I233•

L237•

E238

K239•

L240

K241

G242

Q243

D244

K255

T260

E263

R264

V268

L271

N272

F276

T277

V278

K279

L287

E288

I296•

P303•

K310

R311

E312

Y332

L333

E334

K335

H336

K337

D338

R339•


4 Data and re�nement statistics iO

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

125.27Å 104.18Å 120.56Å90.00◦ 90.00◦ 90.00◦

Depositor

Resolution (Å)49.04 � 2.3849.04 � 2.38

DepositorEDS

% Data completeness(in resolution range)

94.2 (49.04-2.38)91.9 (49.04-2.38)

DepositorEDS

Rmerge 0.10 DepositorRsym (Not available) Depositor

< I/σ(I) > 1 4.29 (at 2.37Å) XtriageRe�nement program PHENIX 1.17.1-3660 Depositor

R, Rfree0.232 , 0.2760.232 , 0.276

DepositorDCC

Rfree test set 1974 re�ections (3.22%) wwPDB-VPWilson B-factor (Å2) 47.2 Xtriage

Anisotropy 0.211 XtriageBulk solvent ksol(e/Å3), Bsol(Å2) 0.31 , 41.3 EDS

L-test for twinning2 < |L| > = 0.47, < L2 > = 0.31 XtriageEstimated twinning fraction 0.025 for l,-k,h Xtriage

Fo,Fc correlation 0.93 EDSTotal number of atoms 11143 wwPDB-VP

Average B, all atoms (Å2) 56.0 wwPDB-VP

Xtriage's analysis on translational NCS is as follows: The analyses of the Patterson function reveals

a signi�cant o�-origin peak that is 29.94 % of the origin peak, indicating pseudo-translational

symmetry. The chance of �nding a peak of this or larger height randomly in a structure without

pseudo-translational symmetry is equal to 1.4222e-03. The detected translational NCS is most

likely also responsible for the elevated intensity ratio.

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:AMP

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 angles

RMSZ #|Z| >5 RMSZ #|Z| >51 A 0.56 0/2755 0.80 9/3710 (0.2%)1 B 0.56 2/2755 (0.1%) 0.82 8/3710 (0.2%)1 C 0.57 1/2755 (0.0%) 0.86 8/3710 (0.2%)1 D 0.60 3/2755 (0.1%) 0.89 19/3710 (0.5%)All All 0.58 6/11020 (0.1%) 0.84 44/14840 (0.3%)

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 21 D 0 2All All 0 4

All (6) bond length outliers are listed below:

Mol Chain Res Type Atoms Z Observed(Å) Ideal(Å)1 D 133 GLU CB-CG 8.24 1.67 1.521 B 115 GLU CG-CD -7.65 1.40 1.511 D 195 ARG CZ-NH1 6.26 1.41 1.331 D 188 CYS CB-SG -6.18 1.71 1.821 B 22 GLU CB-CG -5.92 1.41 1.521 C 339 ARG CG-CD 5.37 1.65 1.51

All (44) bond angle outliers are listed below:

Mol Chain Res Type Atoms Z Observed(o) Ideal(o)1 B 46 ARG NE-CZ-NH2 -10.49 115.06 120.30

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 115 GLU CA-CB-CG -10.40 90.51 113.401 B 46 ARG CG-CD-NE 9.42 131.57 111.801 C 22 GLU CA-CB-CG 9.00 133.19 113.401 D 100 ARG CG-CD-NE 8.50 129.65 111.801 D 195 ARG CB-CG-CD -7.70 91.57 111.601 D 233 ILE CG1-CB-CG2 -7.59 94.71 111.401 A 307 LYS CD-CE-NZ 7.42 128.76 111.701 C 210 LYS CA-CB-CG -7.21 97.53 113.401 D 208 ARG NE-CZ-NH2 -7.07 116.76 120.301 D 100 ARG NE-CZ-NH2 -6.90 116.85 120.301 D 208 ARG NE-CZ-NH1 6.77 123.68 120.301 D 204 HIS N-CA-CB -6.64 98.64 110.601 D 195 ARG NE-CZ-NH2 -6.55 117.02 120.301 D 100 ARG CB-CG-CD -6.54 94.60 111.601 D 100 ARG CA-CB-CG 6.50 127.70 113.401 C 82 ARG NE-CZ-NH2 -6.46 117.07 120.301 B 208 ARG NE-CZ-NH2 -6.46 117.07 120.301 A 339 ARG CB-CG-CD 6.41 128.26 111.601 D 100 ARG CD-NE-CZ 6.32 132.44 123.601 C 42 LYS CD-CE-NZ 6.30 126.18 111.701 A 269 LYS CB-CG-CD -6.18 95.52 111.601 D 195 ARG CA-CB-CG 6.18 126.99 113.401 C 82 ARG NE-CZ-NH1 6.17 123.39 120.301 D 190 ARG CG-CD-NE -6.12 98.95 111.801 A 338 ASP C-N-CA -5.90 106.95 121.701 B 195 ARG CG-CD-NE 5.84 124.07 111.801 A 269 LYS CB-CA-C -5.77 98.86 110.401 C 211 MET CB-CG-SD -5.74 95.18 112.401 A 269 LYS CA-CB-CG 5.74 126.02 113.401 D 210 LYS CA-CB-CG 5.60 125.72 113.401 C 133 GLU CA-CB-CG 5.57 125.66 113.401 D 195 ARG NE-CZ-NH1 -5.54 117.53 120.301 B 208 ARG CA-CB-CG 5.51 125.53 113.401 D 195 ARG NH1-CZ-NH2 5.49 125.44 119.401 A 133 GLU CA-CB-CG -5.49 101.33 113.401 D 99 ASP C-N-CA -5.46 108.04 121.701 A 339 ARG CA-CB-CG -5.40 101.51 113.401 C 164 LYS CD-CE-NZ -5.36 99.37 111.701 B 46 ARG CA-CB-CG 5.35 125.17 113.401 A 338 ASP CB-CA-C -5.30 99.81 110.401 D 190 ARG NE-CZ-NH2 -5.10 117.75 120.301 B 208 ARG NE-CZ-NH1 5.07 122.83 120.30




Mol Chain Res Type Atoms Z Observed(o) Ideal(o)1 D 133 GLU CA-CB-CG 5.06 124.53 113.40

There are no chirality outliers.

All (4) planarity outliers are listed below:

Mol Chain Res Type Group1 B 21 ALA Peptide1 B 46 ARG Sidechain1 D 133 GLU Sidechain1 D 204 HIS Sidechain

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 2708 0 2709 46 01 B 2708 0 2709 37 01 C 2708 0 2708 79 01 D 2708 0 2709 56 02 A 22 0 12 0 02 B 22 0 12 1 02 C 22 0 12 2 02 D 22 0 12 0 03 A 73 0 0 8 03 B 48 0 0 7 03 C 45 0 0 5 03 D 57 0 0 6 0All All 11143 0 10883 212 0

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 10.

All (212) close contacts within the same asymmetric unit are listed below, sorted by their clashmagnitude.

Atom-1 Atom-2Interatomicdistance (Å)

Clashoverlap (Å)

1:D:85:ARG:NH1 1:D:334:GLU:CD 1.99 1.17Continued on next page...

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




Clashoverlap (Å)

1:C:146:ASP:OD1 1:C:190:ARG:NH2 1.77 1.151:D:85:ARG:NH1 1:D:334:GLU:OE1 1.85 1.091:D:85:ARG:NH1 1:D:334:GLU:OE2 1.84 1.091:D:188:CYS:SG 3:D:554:HOH:O 2.13 1.041:B:25:GLU:OE1 3:B:501:HOH:O 1.84 0.941:B:195:ARG:NH1 1:B:197:THR:HG22 1.83 0.921:A:146:ASP:OD2 1:A:190:ARG:NH2 2.05 0.891:A:260:THR:OG1 3:A:501:HOH:O 1.92 0.881:C:145:THR:O 2:C:401:AMP:O3' 1.94 0.851:B:172:ALA:O 3:B:502:HOH:O 1.99 0.791:C:207:ARG:O 1:C:210:LYS:HG2 1.82 0.79

1:D:85:ARG:HH12 1:D:334:GLU:CD 1.71 0.791:B:130:LEU:HB2 1:B:133:GLU:HG3 1.65 0.771:A:336:HIS:HB3 1:A:339:ARG:HD3 1.68 0.751:D:200:ASN:C 1:D:204:HIS:HD2 1.89 0.751:D:332:TYR:OH 1:D:339:ARG:NH1 2.20 0.751:D:80:ARG:NH1 3:D:504:HOH:O 2.21 0.741:B:194:LEU:HD22 1:B:200:ASN:HD21 1.53 0.741:B:99:ASP:OD1 3:B:503:HOH:O 2.06 0.731:A:158:GLU:O 1:A:158:GLU:HG3 1.88 0.731:B:161:LYS:HA 3:B:506:HOH:O 1.88 0.721:C:275:GLY:O 3:C:501:HOH:O 2.07 0.72

1:C:126:ILE:HD13 1:C:131:SER:OG 1.90 0.721:B:195:ARG:HH11 1:B:197:THR:HG22 1.54 0.721:A:238:GLU:OE2 1:A:304:SER:OG 2.08 0.701:A:126:ILE:HD11 1:A:131:SER:OG 1.93 0.681:A:175:SER:O 3:A:502:HOH:O 2.09 0.68

1:D:145:THR:HG21 1:D:175:SER:OG 1.93 0.681:D:193:GLU:OE2 3:D:501:HOH:O 2.11 0.681:D:260:THR:OG1 1:D:263:GLU:HG3 1.94 0.67

1:D:5:LYS:O 3:D:502:HOH:O 2.12 0.671:C:124:PRO:HG2 1:C:339:ARG:NH1 2.09 0.671:A:262:ILE:N 3:A:501:HOH:O 2.27 0.661:C:250:ILE:HB 1:C:259:LEU:HD12 1.76 0.661:A:337:LYS:O 3:A:503:HOH:O 2.15 0.64

1:C:224:LEU:HD23 1:C:250:ILE:HG12 1.79 0.641:D:130:LEU:HD23 1:D:201:ALA:HB3 1.81 0.631:C:265:GLN:HA 1:C:268:VAL:HG12 1.78 0.631:D:335:LYS:HG2 1:D:336:HIS:CD2 2.33 0.631:D:264:ARG:O 1:D:268:VAL:HG23 1.98 0.631:C:259:LEU:HB3 1:C:263:GLU:HG3 1.79 0.63





Clashoverlap (Å)

1:A:133:GLU:CD 1:B:129:ASN:H 2.03 0.621:A:133:GLU:HG3 1:A:134:ILE:N 2.14 0.621:A:133:GLU:OE1 1:B:130:LEU:N 2.33 0.611:A:133:GLU:HG3 1:A:134:ILE:H 1.65 0.611:B:239:LYS:HB2 1:B:306:ASN:HD22 1.66 0.611:A:232:SER:OG 1:A:232:SER:O 2.14 0.601:C:247:LEU:HG 1:C:248:PHE:N 2.15 0.601:A:263:GLU:N 3:A:501:HOH:O 1.96 0.601:D:82:ARG:NH2 3:D:504:HOH:O 2.35 0.601:B:22:GLU:O 1:B:38:LYS:HD3 2.02 0.59

1:C:200:ASN:ND2 1:C:203:TRP:H 1.98 0.591:D:82:ARG:HH11 1:D:337:LYS:HB3 1.67 0.591:B:161:LYS:NZ 1:B:290:ASN:OD1 2.36 0.591:A:209:ASN:HB2 1:A:277:THR:O 2.04 0.581:C:209:ASN:ND2 1:C:211:MET:SD 2.76 0.581:C:250:ILE:HB 1:C:259:LEU:CD1 2.34 0.581:A:336:HIS:O 1:A:339:ARG:HD3 2.04 0.57

1:B:130:LEU:HB2 1:B:133:GLU:CG 2.35 0.571:D:200:ASN:C 1:D:204:HIS:CD2 2.76 0.57

1:B:260:THR:OG1 1:B:263:GLU:HG3 2.04 0.571:C:175:SER:HB3 1:C:190:ARG:HB2 1.87 0.571:A:130:LEU:HD23 1:A:201:ALA:HB3 1.87 0.571:A:224:LEU:HD23 1:A:250:ILE:HG12 1.86 0.571:B:169:VAL:HG13 1:B:311:ARG:HD2 1.86 0.571:C:185:ILE:HG21 1:C:212:ILE:HG13 1.85 0.571:C:262:ILE:HD12 1:C:262:ILE:H 1.69 0.571:B:59:ASP:OD2 1:C:85:ARG:NH1 2.38 0.561:B:238:GLU:OE2 1:B:304:SER:OG 2.22 0.561:C:306:ASN:HB3 1:C:309:VAL:HG12 1.87 0.551:D:312:GLU:HG3 1:D:332:TYR:CE1 2.41 0.551:A:303:PRO:O 1:A:311:ARG:HD3 2.07 0.55

1:D:145:THR:HG23 1:D:145:THR:O 2.06 0.551:C:162:GLY:O 1:C:164:LYS:HE2 2.07 0.55

1:C:180:ARG:NH1 1:C:221:ASN:OD1 2.40 0.551:C:215:LEU:O 3:C:503:HOH:O 2.18 0.55

1:D:33:THR:HG23 1:D:90:LEU:O 2.07 0.551:C:115:GLU:H 1:C:115:GLU:CD 2.11 0.54

1:C:80:ARG:HH22 1:C:338:ASP:C 2.11 0.541:D:244:ASP:OD2 1:D:279:LYS:HE3 2.06 0.541:D:209:ASN:HB2 1:D:277:THR:O 2.08 0.541:A:252:ASP:CG 1:A:255:LYS:HG3 2.29 0.53





Clashoverlap (Å)

1:D:130:LEU:HD11 1:D:233:ILE:CD1 2.39 0.531:C:261:PRO:HG2 1:C:319:LEU:HD23 1.90 0.531:A:103:GLU:O 1:D:310:LYS:NZ 2.38 0.531:B:209:ASN:ND2 1:B:278:VAL:HG22 2.24 0.531:A:133:GLU:OE1 1:B:129:ASN:N 2.42 0.531:C:58:GLU:OE1 1:C:77:ARG:HD3 2.09 0.531:B:237:LEU:HG 1:B:309:VAL:HG11 1.91 0.531:C:231:GLU:HA 1:C:236:ASN:HB2 1.91 0.521:D:271:LEU:HG 1:D:276:PHE:HB2 1.91 0.521:A:1:MET:HG3 1:A:148:GLU:HB2 1.92 0.521:C:178:VAL:HB 1:C:211:MET:HE2 1.92 0.521:C:336:HIS:O 1:C:338:ASP:N 2.42 0.511:C:191:ASN:N 3:C:502:HOH:O 2.15 0.511:C:4:ARG:HB3 1:C:6:LEU:HD23 1.91 0.511:A:336:HIS:HB3 1:A:339:ARG:CD 2.39 0.511:C:147:GLN:O 1:C:326:LYS:HE2 2.11 0.51

1:C:223:ALA:HB3 1:C:251:TYR:HB3 1.91 0.511:B:272:ASN:OD1 1:B:277:THR:HA 2.11 0.501:C:237:LEU:HG 1:C:309:VAL:HG21 1.93 0.501:A:139:PRO:HG2 1:A:142:ILE:HD12 1.93 0.501:D:255:LYS:HE3 1:D:255:LYS:O 2.11 0.501:A:301:ASP:OD1 1:A:302:GLY:N 2.44 0.501:D:185:ILE:HG21 1:D:212:ILE:HG23 1.93 0.501:C:9:ILE:HG22 1:C:109:VAL:HA 1.94 0.501:C:145:THR:N 3:C:508:HOH:O 2.29 0.49

1:A:168:THR:OG1 3:A:504:HOH:O 2.20 0.491:A:133:GLU:CG 1:A:134:ILE:H 2.26 0.491:A:264:ARG:O 1:A:268:VAL:HG23 2.12 0.491:D:183:ASP:OD1 1:D:183:ASP:N 2.40 0.491:D:139:PRO:HB3 1:D:141:PHE:CZ 2.48 0.491:C:197:THR:HB 1:C:200:ASN:HB2 1.95 0.481:C:244:ASP:OD2 1:C:279:LYS:HE3 2.13 0.481:D:130:LEU:HD11 1:D:233:ILE:HD12 1.95 0.481:D:200:ASN:O 1:D:204:HIS:CD2 2.66 0.48

1:D:272:ASN:OD1 1:D:277:THR:HA 2.13 0.481:D:335:LYS:HG2 1:D:336:HIS:CG 2.48 0.481:C:266:SER:O 1:C:269:LYS:HB3 2.13 0.48

1:D:201:ALA:HB1 1:D:243:GLN:OE1 2.12 0.481:B:161:LYS:HG2 3:B:506:HOH:O 2.14 0.481:A:116:ILE:HG13 3:A:527:HOH:O 2.13 0.481:D:82:ARG:NH1 1:D:337:LYS:HB3 2.28 0.48





Clashoverlap (Å)

1:B:239:LYS:HB2 1:B:306:ASN:ND2 2.29 0.481:A:58:GLU:OE2 1:A:77:ARG:NH1 2.46 0.471:C:2:GLY:O 1:C:3:VAL:HB 2.13 0.47

1:C:85:ARG:HH21 1:C:90:LEU:HB2 1.78 0.471:C:174:SER:O 1:C:228:ILE:HG22 2.14 0.471:C:223:ALA:O 1:C:250:ILE:HA 2.14 0.471:D:67:SER:O 3:D:503:HOH:O 2.19 0.47

1:B:134:ILE:HG23 1:B:192:TRP:HB3 1.96 0.471:C:104:LEU:HD11 1:C:117:LEU:HD11 1.97 0.471:A:130:LEU:HD13 1:A:174:SER:OG 2.15 0.471:C:303:PRO:HD2 1:C:311:ARG:NH1 2.30 0.471:D:185:ILE:HD12 1:D:216:GLN:HG3 1.95 0.471:B:135:LEU:HB3 1:B:193:GLU:HG2 1.96 0.471:B:290:ASN:HA 3:B:506:HOH:O 2.14 0.471:A:35:VAL:HG23 1:A:91:SER:HB2 1.96 0.461:C:4:ARG:HG3 1:C:4:ARG:HH11 1.80 0.461:A:147:GLN:O 1:A:326:LYS:HE2 2.15 0.461:C:35:VAL:HG23 1:C:91:SER:HB2 1.97 0.461:D:201:ALA:HA 1:D:204:HIS:HB2 1.96 0.461:C:260:THR:OG1 1:C:263:GLU:HG2 2.14 0.461:C:268:VAL:O 1:C:272:ASN:ND2 2.27 0.46

1:C:221:ASN:HB2 1:C:254:ASP:OD2 2.16 0.461:D:133:GLU:HB3 1:D:195:ARG:HH22 1.81 0.461:D:200:ASN:OD1 1:D:203:TRP:HD1 1.99 0.461:C:62:ARG:NH1 1:C:103:GLU:OE2 2.48 0.461:C:177:THR:OG1 1:C:225:GLN:HG2 2.16 0.451:D:205:ALA:HA 1:D:208:ARG:HG2 1.98 0.451:B:281:VAL:HG21 2:B:401:AMP:N6 2.31 0.45

1:D:2:GLY:C 1:D:4:ARG:H 2.19 0.451:C:218:LEU:HD12 1:C:218:LEU:HA 1.79 0.451:C:40:GLU:OE2 1:C:100:ARG:NH2 2.49 0.451:D:336:HIS:HB3 1:D:339:ARG:HG3 1.98 0.451:C:262:ILE:HD11 1:C:319:LEU:HD22 1.99 0.451:A:133:GLU:CG 1:A:134:ILE:N 2.80 0.451:D:104:LEU:HD11 1:D:117:LEU:HD21 1.98 0.451:A:127:SER:OG 1:A:130:LEU:HG 2.17 0.451:C:73:TYR:OH 3:C:504:HOH:O 2.21 0.451:C:255:LYS:HG3 1:C:257:GLN:HG2 1.98 0.441:C:139:PRO:HB3 1:C:141:PHE:CZ 2.52 0.441:D:201:ALA:C 1:D:204:HIS:HB2 2.37 0.441:D:80:ARG:HD2 1:D:122:TRP:CD2 2.53 0.44





Clashoverlap (Å)

1:D:1:MET:HG2 1:D:2:GLY:H 1.82 0.441:C:260:THR:HB 1:C:319:LEU:O 2.18 0.441:D:101:PHE:HB3 1:D:104:LEU:HD12 2.00 0.431:C:200:ASN:HD22 1:C:203:TRP:HB2 1.82 0.431:D:187:VAL:HB 1:D:203:TRP:CE2 2.52 0.431:C:306:ASN:HB3 1:C:309:VAL:CG1 2.48 0.431:C:267:LEU:O 1:C:271:LEU:HD12 2.19 0.43

1:A:185:ILE:HG21 1:A:212:ILE:HG23 2.01 0.431:C:263:GLU:H 1:C:263:GLU:HG2 1.71 0.431:C:162:GLY:O 1:C:164:LYS:CE 2.67 0.431:A:80:ARG:NH2 3:A:503:HOH:O 2.51 0.431:B:261:PRO:HG2 1:B:319:LEU:HD23 2.01 0.421:B:147:GLN:O 1:B:326:LYS:HE2 2.19 0.421:D:241:LYS:HG3 1:D:241:LYS:O 2.18 0.421:C:142:ILE:HG22 1:C:143:SER:O 2.19 0.421:C:265:GLN:HA 1:C:268:VAL:CG1 2.46 0.421:D:37:LYS:HE3 1:D:37:LYS:HB3 1.94 0.421:A:1:MET:HE2 1:A:3:VAL:O 2.19 0.421:A:40:GLU:OE2 1:A:100:ARG:NH2 2.51 0.421:B:196:GLU:HG3 1:B:203:TRP:CZ2 2.55 0.421:C:315:VAL:HG21 2:C:401:AMP:C6 2.54 0.421:C:142:ILE:HD11 1:C:179:TYR:CD1 2.54 0.421:C:303:PRO:HD2 1:C:311:ARG:HH12 1.84 0.421:C:212:ILE:HG23 1:C:213:GLU:N 2.35 0.421:A:313:GLY:O 1:A:314:LEU:HD23 2.19 0.411:B:127:SER:HB2 1:B:128:THR:H 1.53 0.411:C:200:ASN:HD22 1:C:203:TRP:H 1.66 0.411:C:247:LEU:HD11 1:C:249:ASP:O 2.20 0.411:C:304:SER:HB3 1:C:309:VAL:HG13 2.00 0.411:C:4:ARG:HB3 1:C:6:LEU:CD2 2.50 0.411:A:157:ILE:HA 1:A:157:ILE:HD13 1.93 0.411:B:37:LYS:NZ 3:B:516:HOH:O 2.54 0.411:B:260:THR:HB 1:B:319:LEU:O 2.21 0.411:B:46:ARG:HB3 1:B:98:MET:HG2 2.03 0.411:C:26:CYS:SG 1:C:33:THR:HG23 2.60 0.411:A:26:CYS:SG 1:A:33:THR:HG23 2.61 0.41

1:C:238:GLU:OE2 1:C:304:SER:OG 2.36 0.411:D:68:LYS:HA 1:D:68:LYS:HD2 1.87 0.41

1:D:260:THR:HG23 1:D:263:GLU:OE1 2.20 0.401:C:185:ILE:CG2 1:C:212:ILE:HG13 2.50 0.401:A:217:PHE:CE2 1:C:72:ASP:HB2 2.57 0.40





Clashoverlap (Å)

1:A:2:GLY:O 1:A:3:VAL:HB 2.22 0.401:B:67:SER:O 1:B:70:VAL:HG23 2.21 0.40

1:C:127:SER:HB2 1:C:130:LEU:HD13 2.04 0.401:D:186:GLY:HA3 1:D:193:GLU:OE1 2.22 0.401:B:80:ARG:HD2 1:B:122:TRP:CE2 2.56 0.401:D:287:LEU:HD23 1:D:288:GLU:C 2.42 0.40

There are no symmetry-related clashes.

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 337/340 (99%) 325 (96%) 11 (3%) 1 (0%) 41 53

1 B 337/340 (99%) 318 (94%) 18 (5%) 1 (0%) 41 53

1 C 337/340 (99%) 321 (95%) 13 (4%) 3 (1%) 17 23

1 D 337/340 (99%) 319 (95%) 17 (5%) 1 (0%) 41 53

All All 1348/1360 (99%) 1283 (95%) 59 (4%) 6 (0%) 34 46

All (6) Ramachandran outliers are listed below:

Mol Chain Res Type1 B 130 LEU1 C 196 GLU1 C 337 LYS1 D 3 VAL1 A 3 VAL1 C 3 VAL

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 292/293 (100%) 281 (96%) 11 (4%) 33 49

1 B 292/293 (100%) 288 (99%) 4 (1%) 67 81

1 C 292/293 (100%) 285 (98%) 7 (2%) 49 66

1 D 292/293 (100%) 286 (98%) 6 (2%) 53 70

All All 1168/1172 (100%) 1140 (98%) 28 (2%) 49 66

All (28) residues with a non-rotameric sidechain are listed below:

Mol Chain Res Type1 A 67 SER1 A 82 ARG1 A 85 ARG1 A 115 GLU1 A 127 SER1 A 164 LYS1 A 195 ARG1 A 208 ARG1 A 232 SER1 A 241 LYS1 A 285 ASP1 B 85 ARG1 B 195 ARG1 B 204 HIS1 B 287 LEU1 C 34 CYS1 C 115 GLU1 C 161 LYS1 C 195 ARG1 C 204 HIS1 C 249 ASP1 C 285 ASP1 D 100 ARG1 D 106 SER


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



Mol Chain Res Type1 D 127 SER1 D 135 LEU1 D 190 ARG1 D 255 LYS

Some sidechains can be �ipped to improve hydrogen bonding and reduce clashes. All (5) suchsidechains are listed below:

Mol Chain Res Type1 B 129 ASN1 C 69 GLN1 C 76 GLN1 C 200 ASN1 D 204 HIS

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 monosaccharides in this entry.

5.6 Ligand geometry iO

4 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).

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

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




Mol Type Chain Res LinkBond lengths Bond angles

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

2 AMP C 401 1 18,24,25 1.01 2 (11%) 18,35,38 1.27 2 (11%)

2 AMP D 401 1 18,24,25 0.97 1 (5%) 18,35,38 1.45 4 (22%)

2 AMP A 401 1 18,24,25 0.87 1 (5%) 18,35,38 1.32 1 (5%)

2 AMP B 401 1 18,24,25 1.18 2 (11%) 18,35,38 1.61 3 (16%)

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.

Mol Type Chain Res Link Chirals Torsions Rings2 AMP C 401 1 - 2/3/25/26 0/3/3/32 AMP D 401 1 - 1/3/25/26 0/3/3/32 AMP A 401 1 - 1/3/25/26 0/3/3/32 AMP B 401 1 - 2/3/25/26 0/3/3/3

All (6) bond length outliers are listed below:

Mol Chain Res Type Atoms Z Observed(Å) Ideal(Å)2 B 401 AMP C2-N3 2.86 1.36 1.322 B 401 AMP C5-C4 2.81 1.48 1.402 C 401 AMP C5-C4 2.55 1.47 1.402 D 401 AMP C5-C4 2.34 1.47 1.402 A 401 AMP C5-C4 2.10 1.46 1.402 C 401 AMP C2-N3 2.01 1.35 1.32

All (10) bond angle outliers are listed below:

Mol Chain Res Type Atoms Z Observed(o) Ideal(o)2 B 401 AMP C1'-N9-C4 4.12 133.88 126.642 C 401 AMP N3-C2-N1 -3.60 123.05 128.682 B 401 AMP C4-C5-N7 -3.39 105.87 109.402 A 401 AMP N3-C2-N1 -3.23 123.63 128.682 D 401 AMP C1'-N9-C4 3.14 132.16 126.642 D 401 AMP C4-C5-N7 -2.96 106.31 109.402 D 401 AMP N3-C2-N1 -2.86 124.21 128.682 C 401 AMP C4-C5-N7 -2.68 106.61 109.402 B 401 AMP C3'-C2'-C1' 2.18 104.26 100.982 D 401 AMP C3'-C2'-C1' 2.10 104.15 100.98

There are no chirality outliers.


All (6) torsion outliers are listed below:

Mol Chain Res Type Atoms2 C 401 AMP C4'-C5'-O5'-P2 D 401 AMP C4'-C5'-O5'-P2 A 401 AMP C4'-C5'-O5'-P2 B 401 AMP C4'-C5'-O5'-P2 C 401 AMP C3'-C4'-C5'-O5'2 B 401 AMP C3'-C4'-C5'-O5'

There are no ring outliers.

2 monomers are involved in 3 short contacts:

Mol Chain Res Type Clashes Symm-Clashes2 C 401 AMP 2 02 B 401 AMP 1 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 AMP C 401

Bond lengths Bond angles

Torsions Rings

Ligand AMP D 401


Torsions Rings


Ligand AMP A 401


Torsions Rings

Ligand AMP B 401


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 339/340 (99%) 0.12 9 (2%) 54 56 29, 49, 71, 85 0

1 B 339/340 (99%) 0.34 20 (5%) 22 24 38, 59, 78, 100 0

1 C 339/340 (99%) 0.58 29 (8%) 10 11 33, 64, 87, 104 0

1 D 339/340 (99%) 0.29 15 (4%) 34 37 31, 53, 80, 90 0

All All 1356/1360 (99%) 0.33 73 (5%) 25 28 29, 55, 81, 104 0

All (73) RSRZ outliers are listed below:

Mol Chain Res Type RSRZ1 C 3 VAL 5.81 D 339 ARG 5.71 B 128 THR 5.61 D 2 GLY 5.31 C 237 LEU 5.11 C 128 THR 5.01 C 2 GLY 4.71 A 339 ARG 4.61 C 187 VAL 4.11 C 211 MET 4.01 D 199 THR 3.91 C 131 SER 3.81 B 108 GLN 3.71 B 21 ALA 3.71 C 224 LEU 3.61 C 127 SER 3.41 D 130 LEU 3.41 D 195 ARG 3.41 C 196 GLU 3.41 B 290 ASN 3.41 C 198 ALA 3.3


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

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



Mol Chain Res Type RSRZ1 D 198 ALA 3.31 B 2 GLY 3.11 C 130 LEU 3.11 C 278 VAL 3.11 B 308 ASN 3.01 B 1 MET 3.01 C 305 LEU 2.91 B 303 PRO 2.91 C 1 MET 2.81 C 212 ILE 2.81 C 250 ILE 2.81 B 129 ASN 2.81 C 192 TRP 2.81 B 126 ILE 2.71 C 203 TRP 2.61 C 339 ARG 2.61 C 141 PHE 2.61 B 22 GLU 2.61 A 338 ASP 2.51 C 218 LEU 2.51 B 195 ARG 2.51 A 198 ALA 2.41 C 213 GLU 2.41 D 239 LYS 2.41 A 1 MET 2.41 A 131 SER 2.41 A 130 LEU 2.31 D 303 PRO 2.31 B 86 LEU 2.31 C 179 TYR 2.31 B 165 PHE 2.31 B 136 GLY 2.31 D 296 ILE 2.31 A 127 SER 2.31 B 198 ALA 2.31 D 101 PHE 2.31 D 237 LEU 2.21 D 204 HIS 2.21 C 319 LEU 2.21 C 271 LEU 2.21 B 127 SER 2.21 A 239 LYS 2.2




Mol Chain Res Type RSRZ1 B 208 ARG 2.21 C 178 VAL 2.11 C 195 ARG 2.11 D 213 GLU 2.11 D 233 ILE 2.11 B 240 LEU 2.01 A 126 ILE 2.01 D 108 GLN 2.01 B 46 ARG 2.01 C 183 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 monosaccharides in this entry.

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 AMP C 401 22/23 0.93 0.14 50,61,66,71 02 AMP D 401 22/23 0.93 0.13 34,47,63,67 02 AMP A 401 22/23 0.95 0.13 36,42,48,50 02 AMP B 401 22/23 0.95 0.12 44,49,52,54 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.

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




Electron density around AMP C 401:

2mFo-DFc (at 0.7 rmsd) in gray

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

and green (positive)

Electron density around AMP D 401:





Electron density around AMP A 401:





Electron density around AMP B 401:




6.5 Other polymers iO

There are no such residues in this entry.


full wwpdb x-ray structure validation report o i · 2020. 8. 8. · rst graphic for a chain...

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