Full wwPDB X-ray Structure Validation Report O i · 2020. 5. 31. · Full wwPDB X-ray Structure...

Full wwPDB X-ray Structure Validation Report iO

May 18, 2020 � 02:34 pm BST

PDB ID : 2FE8Title : SARS coronavirus papain-like protease: structure of a viral deubiquitinating

enzymeAuthors : Ratia, K.; Santarsiero, B.D.; Mesecar, A.D.

Deposited on : 2005-12-15Resolution : 1.85 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

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

Full wwPDB X-ray Structure Validation Report 2FE8

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 1.85 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 2469 (1.86-1.86)Clashscore 141614 2625 (1.86-1.86)

Ramachandran outliers 138981 2592 (1.86-1.86)Sidechain outliers 138945 2592 (1.86-1.86)RSRZ outliers 127900 2436 (1.86-1.86)

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


2 Entry composition iO

There are 5 unique types of molecules in this entry. The entry contains 7978 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 Replicase polyprotein 1ab.

Mol Chain Residues Atoms ZeroOcc AltConf Trace

1 A 315Total C N O S2482 1574 412 478 18

0 0 0

1 B 314Total C N O S2473 1568 411 476 18

0 0 0

1 C 313Total C N O S2466 1564 410 474 18

0 0 0

There are 3 discrepancies between the modelled and reference sequences:

Chain Residue Modelled Actual Comment ReferenceA 1 MET - INITIATING METHIONINE UNP P59641B 1 MET - INITIATING METHIONINE UNP P59641C 1 MET - INITIATING METHIONINE UNP P59641

Molecule 2 is ZINC ION (three-letter code: ZN) (formula: Zn).

Mol Chain Residues Atoms ZeroOcc AltConf

2 B 1Total Zn1 1

0 0

2 A 1Total Zn1 1

0 0

2 C 1Total Zn1 1

0 0

Molecule 3 is BROMIDE ION (three-letter code: BR) (formula: Br).


3 B 3Total Br3 3

0 0

3 A 3Total Br3 3

0 0

Continued on next page...

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


Continued from previous page...


3 C 3Total Br3 3

0 0

Molecule 4 is SULFATE ION (three-letter code: SO4) (formula: O4S).


4 A 1Total O S5 4 1

0 0

4 B 1Total O S5 4 1

0 0

4 C 1Total O S5 4 1

0 0

Molecule 5 is water.


5 A 206Total O206 206

0 0

5 B 177Total O177 177

0 0

5 C 147Total O147 147

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: Replicase polyprotein 1ab

Chain A:

M1

D23

M26

V42

I45

K46

P47

H48

F70•

L81

T103

K127

F128

N129

A130

Q134

Y137

Y138•

R141

A142

G143

T171

Q175

N178

V188

K191•

H192

T197

V203

E204

M207

Y214

I223

P224

C225•

V226•

C227•

G228•

R229•

D230•

Q233

Q237

Q238

N263

G267

L283

M294

K307

T312

I315


Chain B:

M1

K4

T5

I6

V22

D23

M24

S25

M26

V49

E52

R66

D77

E78•

G82

R83

H90

L121

Y137

R141

F148

I152

V160

T171

H172

L173

L174

Q175

E204

P224

P249

A250

E251

N263

E264

Y265

T266

G267•

N268

Y269•

Q270•

C271•

G272•

L283

Y284

R285

E296

T302

K307

T314•

ILE


Chain C:

M1•

E2•

V3•

F32

G39

V58

R66

L76

D77

E78

M85

N157

D165

E168

H172

L173

N187

V188

V189

C190

K191•

H192•

Q195

K196

T197

L200

Y208

I223

V226•

C227

G228•

R229•

Q233

P249

Q255

L260

N263

E264

Y265

Y269•

G272

T302

K307

T313•

THR

ILE

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


4 Data and re�nement statistics iO

Property Value SourceSpace group C 1 2 1 DepositorCell constantsa, b, c, α, β, γ

142.87Å 103.06Å 91.73Å90.00◦ 111.15◦ 90.00◦

Depositor

Resolution (Å)20.00 � 1.8545.24 � 1.84

DepositorEDS

% Data completeness(in resolution range)

97.7 (20.00-1.85)96.9 (45.24-1.84)

DepositorEDS

Rmerge 0.08 DepositorRsym (Not available) Depositor

< I/σ(I) > 1 2.76 (at 1.84Å) XtriageRe�nement program CNS Depositor

R, Rfree0.201 , 0.2290.200 , 0.228

DepositorDCC

Rfree test set 5203 re�ections (5.02%) wwPDB-VPWilson B-factor (Å2) 25.2 Xtriage

Anisotropy 0.176 XtriageBulk solvent ksol(e/Å3), Bsol(Å2) 0.36 , 45.0 EDS

L-test for twinning2 < |L| > = 0.50, < L2 > = 0.33 Xtriage

Estimated twinning fraction

0.008 for -1/2*h+1/2*k+l,1/2*h-1/2*k+l,1/2*h+1/2*k

0.014 for -1/2*h-1/2*k+l,-1/2*h-1/2*k-l,1/2*h-1/2*k

Xtriage

Fo,Fc correlation 0.95 EDSTotal number of atoms 7978 wwPDB-VP

Average B, all atoms (Å2) 28.0 wwPDB-VP

Xtriage's analysis on translational NCS is as follows: The largest o�-origin peak in the Pattersonfunction is 4.23% 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: ZN,SO4, BR

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 0/2537 0.70 0/34411 B 0.47 0/2528 0.67 0/34301 C 0.46 0/2521 0.66 0/3420All All 0.48 0/7586 0.68 0/10291

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 C 0 1

There are no bond length outliers.

There are no bond angle outliers.

There are no chirality outliers.

All (1) planarity outliers are listed below:

Mol Chain Res Type Group1 C 269 TYR 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.

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


Mol Chain Non-H H(model) H(added) Clashes Symm-Clashes1 A 2482 0 2425 34 01 B 2473 0 2414 31 01 C 2466 0 2407 29 02 A 1 0 0 0 02 B 1 0 0 0 02 C 1 0 0 0 03 A 3 0 0 1 03 B 3 0 0 0 03 C 3 0 0 0 04 A 5 0 0 0 04 B 5 0 0 0 04 C 5 0 0 0 05 A 206 0 0 2 05 B 177 0 0 3 05 C 147 0 0 4 0All All 7978 0 7246 87 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 6.

All (87) close contacts within the same asymmetric unit are listed below, sorted by their clashmagnitude.

Atom-1 Atom-2Interatomicdistance (Å)

Clashoverlap (Å)

1:A:188:VAL:HG13 1:A:223:ILE:HD11 1.53 0.881:C:39:GLY:HA2 1:C:85:MET:HE1 1.64 0.791:C:39:GLY:HA2 1:C:85:MET:CE 2.14 0.771:B:249:PRO:HG3 1:B:302:THR:CG2 2.16 0.751:A:229:ARG:HG3 1:A:230:ASP:H 1.55 0.711:A:130:ALA:O 1:A:134:GLN:HG3 1.92 0.691:A:23:ASP:HB3 1:A:26:MET:HE3 1.77 0.661:B:78:GLU:HG3 1:C:78:GLU:HG3 1.78 0.651:B:249:PRO:HG3 1:B:302:THR:HG22 1.78 0.651:A:45:ILE:HD11 1:A:48:HIS:NE2 2.12 0.641:B:307:LYS:HE3 5:B:441:HOH:O 1.96 0.641:B:270:GLN:HG2 1:C:208:TYR:CE1 2.33 0.641:A:23:ASP:HB3 1:A:26:MET:CE 2.29 0.621:A:229:ARG:HG3 1:A:230:ASP:N 2.13 0.621:A:223:ILE:HD13 1:A:233:GLN:HB2 1.81 0.621:B:268:ASN:O 1:B:272:GLY:N 2.34 0.61

1:C:223:ILE:HD13 1:C:233:GLN:HB2 1.84 0.591:B:270:GLN:HG2 1:C:208:TYR:CD1 2.37 0.591:C:265:TYR:OH 1:C:272:GLY:HA3 2.01 0.59





Clashoverlap (Å)

1:A:237:GLN:HG3 1:A:312:THR:HG22 1.83 0.591:A:191:LYS:HB2 1:A:229:ARG:HH12 1.68 0.581:C:191:LYS:HE3 1:C:229:ARG:HD2 1.85 0.571:A:204:GLU:HG3 5:A:486:HOH:O 2.05 0.561:C:265:TYR:CZ 1:C:272:GLY:HA3 2.41 0.561:C:58:VAL:HG22 5:C:386:HOH:O 2.05 0.551:C:191:LYS:HE3 1:C:229:ARG:CD 2.36 0.551:B:66:ARG:HD3 5:B:376:HOH:O 2.07 0.551:B:249:PRO:HG3 1:B:302:THR:HG21 1.89 0.551:A:315:ILE:OXT 1:A:315:ILE:HD12 2.07 0.541:A:203:VAL:HG12 1:A:207:MET:HE2 1.89 0.541:A:23:ASP:OD2 1:A:26:MET:HE2 2.08 0.531:A:192:HIS:HB2 1:A:229:ARG:HH22 1.74 0.531:A:45:ILE:HG12 1:A:46:LYS:O 2.08 0.531:A:134:GLN:HA 3:A:318:BR:BR 2.63 0.521:A:42:VAL:HB 1:A:45:ILE:CG2 2.40 0.521:B:23:ASP:HB3 1:B:26:MET:HE3 1.92 0.511:B:204:GLU:HG3 5:B:432:HOH:O 2.11 0.511:B:82:GLY:HA3 1:C:76:LEU:CD1 2.41 0.511:C:157:ASN:HB3 5:C:443:HOH:O 2.10 0.511:C:249:PRO:HG3 1:C:302:THR:CG2 2.41 0.511:B:283:LEU:HD12 1:B:296:GLU:HA 1.93 0.511:A:188:VAL:CG1 1:A:223:ILE:HD11 2.34 0.501:B:49:VAL:HG13 1:B:52:GLU:OE2 2.12 0.49

1:B:4:LYS:O 1:B:24:MET:HG2 2.12 0.491:C:39:GLY:HA2 1:C:85:MET:HE3 1.94 0.491:C:187:ASN:OD1 1:C:197:THR:HG22 2.12 0.491:B:268:ASN:OD1 1:B:269:TYR:HD1 1.96 0.491:C:189:VAL:HG22 1:C:195:GLN:HB3 1.95 0.491:C:223:ILE:CD1 1:C:233:GLN:HB2 2.42 0.481:B:152:ILE:HG12 1:B:173:LEU:HD11 1.95 0.481:A:23:ASP:CB 1:A:26:MET:CE 2.92 0.481:B:266:THR:O 1:B:272:GLY:HA2 2.13 0.481:B:6:ILE:HG13 1:B:22:VAL:HG22 1.96 0.471:B:268:ASN:OD1 1:B:269:TYR:N 2.48 0.47

1:B:4:LYS:C 1:B:24:MET:HG2 2.34 0.471:A:23:ASP:CB 1:A:26:MET:HE2 2.44 0.471:B:78:GLU:HG3 1:C:78:GLU:CG 2.45 0.471:B:171:THR:O 1:B:175:GLN:HG2 2.14 0.47

1:C:249:PRO:HG3 1:C:302:THR:HG21 1.96 0.461:A:42:VAL:O 1:A:45:ILE:HG22 2.16 0.46





Clashoverlap (Å)

1:A:137:TYR:CE2 1:A:141:ARG:HD2 2.50 0.461:C:66:ARG:HD2 5:C:437:HOH:O 2.17 0.461:C:191:LYS:HE3 1:C:229:ARG:CG 2.47 0.441:A:171:THR:O 1:A:175:GLN:HG3 2.18 0.431:B:148:PHE:CE2 1:B:152:ILE:HD11 2.52 0.431:C:227:CYS:SG 1:C:229:ARG:HB2 2.57 0.431:C:32:PHE:HB3 1:C:58:VAL:HG21 2.00 0.431:A:267:GLY:HA2 1:B:224:PRO:HG3 2.00 0.431:C:196:LYS:N 1:C:196:LYS:HD2 2.34 0.43

1:A:103:THR:OG1 1:A:143:GLY:HA2 2.18 0.431:A:214:TYR:OH 1:A:238:GLN:HG2 2.20 0.411:A:229:ARG:HH11 1:A:229:ARG:HG2 1.85 0.411:C:172:HIS:HB2 5:C:428:HOH:O 2.20 0.411:A:128:PHE:O 1:A:134:GLN:HG2 2.21 0.41

1:A:197:THR:HG21 1:A:315:ILE:HD11 2.03 0.411:A:45:ILE:HG12 1:A:46:LYS:N 2.35 0.411:A:127:LYS:HE3 1:A:178:ASN:HD22 1.86 0.401:A:283:LEU:HB2 1:A:294:MET:O 2.22 0.401:B:121:LEU:HD11 1:B:173:LEU:HD13 2.03 0.401:B:23:ASP:HB3 1:B:26:MET:CE 2.51 0.401:A:307:LYS:HE3 5:A:473:HOH:O 2.20 0.401:C:165:ASP:HB3 1:C:168:GLU:HB3 2.03 0.401:B:137:TYR:CE2 1:B:141:ARG:HD2 2.56 0.401:B:77:ASP:OD1 1:B:83:ARG:NH2 2.53 0.401:C:260:LEU:HG 1:C:307:LYS:HG3 2.03 0.401:B:90:HIS:HB2 1:B:160:VAL:HG21 2.04 0.401:B:270:GLN:O 1:C:200:LEU:HD11 2.22 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.

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


Mol Chain Analysed Favoured Allowed Outliers Percentiles

1 A 313/315 (99%) 307 (98%) 6 (2%) 0 100 100

1 B 312/315 (99%) 304 (97%) 7 (2%) 1 (0%) 41 26

1 C 311/315 (99%) 301 (97%) 10 (3%) 0 100 100

All All 936/945 (99%) 912 (97%) 23 (2%) 1 (0%) 51 36

All (1) Ramachandran outliers are listed below:

Mol Chain Res Type1 B 269 TYR

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 272/272 (100%) 267 (98%) 5 (2%) 59 45

1 B 271/272 (100%) 265 (98%) 6 (2%) 52 36

1 C 270/272 (99%) 264 (98%) 6 (2%) 52 36

All All 813/816 (100%) 796 (98%) 17 (2%) 53 38

All (17) residues with a non-rotameric sidechain are listed below:

Mol Chain Res Type1 A 45 ILE1 A 81 LEU1 A 229 ARG1 A 263 ASN1 A 315 ILE1 B 66 ARG1 B 251 GLU1 B 263 ASN1 B 264 GLU1 B 270 GLN1 B 285 ARG1 C 173 LEU


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



Mol Chain Res Type1 C 196 LYS1 C 255 GLN1 C 263 ASN1 C 269 TYR1 C 313 THR

Some sidechains can be �ipped to improve hydrogen bonding and reduce clashes. There are nosuch sidechains identi�ed.

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

Of 15 ligands modelled in this entry, 12 are monoatomic - leaving 3 for Mogul analysis.

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| > 24 SO4 C 320 - 4,4,4 0.27 0 6,6,6 0.18 04 SO4 B 320 - 4,4,4 0.24 0 6,6,6 0.19 04 SO4 A 320 - 4,4,4 0.27 0 6,6,6 0.18 0

There are no bond length outliers.

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


There are no bond angle outliers.

There are no chirality outliers.

There are no torsion outliers.

There are no ring outliers.

No monomer is involved in short contacts.

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#nonstandard_residues_and_ligandshttps://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>2 OWAB(Å2) Q



Mol Chain Res Type RSRZ1 B 267 GLY 2.31 A 191 LYS 2.31 C 228 GLY 2.3

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.

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

Full wwPDB X-ray Structure Validation Report O i · 2020. 5. 31. · Full wwPDB X-ray Structure...

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