iFull wwPDB X-ray Structure Validation Report ○Jun 18, 2024 – 07:24 AM EDTPDB ID : 5R7Z
Title : PanDDA analysis group deposition – Crystal Structure of SARS-CoV-2 main
protease in complex with Z1220452176
Authors : Fearon, D.; Powell, A.J.; Douangamath, A.; Owen, C.D.; Wild, C.; Krojer, T.;
Lukacik, P.; Strain-Damerell, C.M.; Walsh, M.A.; von Delft, F.
Deposited on : 2020-03-03
Resolution : 1.59 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.org
A user guide is available athttps://www.wwpdb.org/validation/2017/XrayValidationReportHelp
i symbol.
with specific help available everywhere you see the ○The types of validation reports are described at
http://www.wwpdb.org/validation/2017/FAQs#types.

i were used in the production of this report:
The following versions of software and data (see references ○)MolProbity
Mogul
Xtriage (Phenix)
EDS
buster-report
Percentile statistics
Refmac
CCP4
Ideal geometry (proteins)
Ideal geometry (DNA, RNA)Validation Pipeline (wwPDB-VP)

::
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4.02b-467
1.8.5 (274361), CSD as541be (2020)
1.13
2.37.1
1.1.7 (2018)20191225.v01 (using entries in the PDB archive December 25th 2019)
5.8.0158
7.0.044 (Gargrove)
Engh & Huber (2001)
Parkinson et al. (1996)
2.37.1

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5R7Zi
Overall quality at a glance ○The following experimental techniques were used to determine the structure:
X-RAY DIFFRACTION
The reported resolution of this entry is 1.59 Å.
Percentile scores (ranging between 0-100) for global validation metrics of the entry are shown in
the following graphic. The table shows the number of entries on which the scores are based.

MetricRf reeClashscore
Ramachandran outliers
Sidechain outliers
RSRZ outliers

Whole archive(#Entries)
130704141614138981138945127900Similar resolution(#Entries, resolution range(Å))
3398 (1.60-1.60)
3665 (1.60-1.60)
3564 (1.60-1.60)
3563 (1.60-1.60)
3321 (1.60-1.60)

The table below summarises the geometric issues observed across the polymeric chains and their
fit to the electron density. The red, orange, yellow and green segments of the lower bar indicate
the fraction of residues that contain outliers for >=3, 2, 1 and 0 types of geometric quality
criteria 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 dot
representing fractions <=5% The upper red bar (where present) indicates the fraction of residues
that have poor fit to the electron density. The numeric value is given above the bar.
MolChain

Length1

A306

Quality of chain

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5R7ZiEntry composition ○There are 4 unique types of molecules in this entry. The entry contains 2730 atoms, of which 0
are hydrogens and 0 are deuteriums.
In the tables below, the ZeroOcc column contains the number of atoms modelled with zero occupancy, the AltConf column contains the number of residues with at least one atom in alternate
conformation and the Trace column contains the number of residues modelled with at most 2atoms.
• Molecule 1 is a protein called 3C-like proteinase.
Mol

ChainResidues

1A304

Atoms
TotalCN
2370 1498 403

O447

S22ZeroOcc

AltConf

Trace030• Molecule 2 is DIMETHYL SULFOXIDE (three-letter code: DMS) (formula: C2 H6 OS).

Mol

ChainResidues

2A

12A

12A

12A

1

Atoms
Total C O
42 1
Total C O
42 1
Total C O
42 1
Total C O
42 1S
1S
1S
1S
1

ZeroOcc

AltConf00000000• Molecule 3 is {N}-[2-(5-fluoranyl-1 {H}-indol-3-yl)ethyl]ethanamide (three-letter code:HWH) (formula: C12 H13 FN2 O) (labeled as "Ligand of Interest" by depositor).

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MolChainResidues

3A

1

Total
16

Atoms
C F N
12 1 2O
1

ZeroOcc

AltConf00• Molecule 4 is water.
MolChainResidues

4A

328

Atoms
Total O328 328

ZeroOcc

AltConf

005R7Z

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5R7ZiResidue-property plots ○These plots are drawn for all protein, RNA, DNA and oligosaccharide chains in the entry. The
first 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 criteria
for 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 fit to the electron density (RSRZ > 2). Stretches of 2or more consecutive residues without any outlier are shown as a green connector. Residues present
in the sample, but not in the model, are shown in grey.
• Molecule 1: 3C-like proteinase

•

•

D216
R217

N221

I200

•
••
T190
A191
Q192

G179

•
H163
H164
M165
E166

•
V157

Y154

G149

S144

P122

Y118

S113
V114
L115

G109
Q110

Y101

T98

N95

V86

•
•
•
R298

G302
V303
T304
PHE
GLN

R60

Q69
A70
G71
N72
V73
P293
F294

L286
L287
E288

I249

K236

•

M49

H41

S1

L27

•
•

Chain A:

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5R7Z

i
Data and refinement statistics ○Property
Space group
Cell constantsa, b, c, α, β, γResolution (Å)% Data completeness(in resolution range)
RmergeRsym< I/σ(I) > 1
Refinement program
R, Rf ree
Rf ree test set
Wilson B-factor (Å2 )Anisotropy
Bulk solvent ksol (e/Å3 ), Bsol (Å2 )L-test for twinning2
Estimated twinning fraction
Fo ,Fc correlation
Total number of atoms
Average B, all atoms (Å2 )

Value
C121
112.09Å 52.51Å 44.38Å
90.00◦ 102.94◦ 90.00◦
54.62 – 1.59
54.62 – 1.59
98.9 (54.62-1.59)
98.9 (54.62-1.59)
0.10(Not available)
1.06 (at 1.59Å)REFMAC 5.8.0238
0.190 , 0.233
0.210 , 0.250
1657 reflections (4.94%)
17.7
0.455
0.33 , 40.9
< |L| > = 0.50, < L2 > = 0.34
No twinning to report.
0.96
2730
26.0

SourceDepositor
Depositor
Depositor
EDS
Depositor
EDS
Depositor
Depositor
Xtriage
Depositor
DepositorDCC
wwPDB-VP
Xtriage
Xtriage
EDS
Xtriage
XtriageEDS
wwPDB-VP
wwPDB-VP

Xtriage’s analysis on translational NCS is as follows: The largest off-origin peak in the Patterson function is 10.29% of the height of the origin peak. No significant pseudotranslation is detected.

Intensities estimated from amplitudes.
Theoretical 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.
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i
Model quality ○5.1

iStandard geometry ○Bond lengths and bond angles in the following residue types are not validated in this section:
DMS, HWH
The Z score for a bond length (or angle) is the number of standard deviations the observed value
is 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).
MolChain

1A

Bond lengths
RMSZ #|Z| >50.66
0/2422

Bond angles
RMSZ #|Z| >50.82
0/3293

There are no bond length outliers.
There are no bond angle outliers.
There are no chirality outliers.
There are no planarity outliers.

5.2iToo-close contacts ○In the following table, the Non-H and H(model) columns list the number of non-hydrogen atoms
and 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 within
the asymmetric unit, whereas Symm-Clashes lists symmetry-related clashes.
Mol12
34All

ChainAAAAAll

Non-H2370
16163282730

H(model)
00000H(added)
2313
24002337

Clashes2230722Symm-Clashes
00033

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 5.
All (22) close contacts within the same asymmetric unit are listed below, sorted by their clashmagnitude.

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Atom-1Atom-2

1:A:110:GLN:HG3
1:A:294:PHE:CD2
1:A:166:GLU:HB2
1:A:288:GLU:OE1
1:A:217:ARG:NH2
1:A:70:ALA:O
1:A:236:LYS:NZ
1:A:110:GLN:NE2
1:A:298:ARG:HG3
1:A:115:LEU:HD11
1:A:118:TYR:CE1
1:A:60:ARG:C
1:A:298:ARG:HD2
1:A:109:GLY:HA2
1:A:101:TYR:HA
1:A:86:VAL:HG13
1:A:95:ASN:HB3
1:A:163:HIS:NE2
1:A:286:LEU:HD12
1:A:113:SER:O
1:A:249:ILE:HG22
1:A:69:GLN:HE21

4:A:703:HOH:O
4:A:658:HOH:O
2:A:405:DMS:H21
4:A:501:HOH:O
4:A:502:HOH:O
1:A:73[A]:VAL:HG12
4:A:506:HOH:O
4:A:505:HOH:O
1:A:303:VAL:HB
1:A:122:PRO:HB3
1:A:144:SER:HB3
4:A:599:HOH:O
2:A:402:DMS:O
1:A:200:ILE:HD13
1:A:157:VAL:O
1:A:179:GLY:HA2
1:A:98:THR:OG1
2:A:405:DMS:C2
1:A:286:LEU:C
1:A:149:GLY:HA2
1:A:293:PRO:HG2
1:A:72:ASN:HA

Interatomic
distance (Å)
1.54
2.30
1.64
2.12
2.26
1.96
2.33
2.32
1.90
1.90
2.45
2.51
2.16
1.97
2.15
2.00
2.20
2.83
2.41
2.22
2.03
1.86

5R7Z

Clash
overlap (Å)
1.07
0.83
0.79
0.67
0.66
0.66
0.61
0.61
0.54
0.53
0.52
0.49
0.46
0.46
0.46
0.43
0.42
0.42
0.410.40
0.40
0.40

All (3) symmetry-related close contacts are listed below. The label for Atom-2 includes the symmetry operator and encoded unit-cell translations to be applied.
Atom-1Atom-2

4:A:821:HOH:O
4:A:679:HOH:O
4:A:503:HOH:O

4:A:821:HOH:O[2_554]
4:A:725:HOH:O[4_556]
4:A:540:HOH:O[2_554]

5.3

iTorsion angles ○

5.3.1

i
Protein backbone ○Interatomic
distance (Å)
1.94
2.11
2.19

Clashoverlap (Å)
0.26
0.09
0.01

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

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MolChainAnalysed

Favoured

AllowedOutliers

1

A

305/306 (100%)

299 (98%)

5 (2%)

1 (0%)

5R7Z

Percentiles
41

21

All (1) Ramachandran outliers are listed below:Mol1ChainARes154

TypeTYR

5.3.2

iProtein sidechains ○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.
MolChainAnalysed

RotamericOutliers

1A

264/263 (100%)

261 (99%)

3 (1%)

Percentiles
73

57

All (3) residues with a non-rotameric sidechain are listed below:
Mol111ChainAAARes
1
27
41TypeSERLEUHIS

Sometimes sidechains can be flipped to improve hydrogen bonding and reduce clashes. All (5) suchsidechains are listed below:Mol11111ChainAAA
A
ARes
1941
119
228
238

5.3.3

i
RNA ○TypeGLNHISASNASNASN

There are no RNA molecules in this entry.

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5R7Zi
Non-standard residues in protein, DNA, RNA chains ○There are no non-standard protein/DNA/RNA residues in this entry.

5.5iCarbohydrates ○There are no monosaccharides in this entry.

5.6iLigand geometry ○5 ligands are modelled in this entry.
In the following table, the Counts columns list the number of bonds (or angles) for which Mogul
statistics 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

TypeChainRes

Link

32222

HWH
DMS
DMS
DMS
DMS

A
A
A
A
A

404
402
401
403
405

-

Bond lengths
Counts RMSZ #|Z| > 2
16,17,17
1.58
3 (18%)
3,3,30.28
03,3,30.27
03,3,30.38
03,3,30.22
0Bond angles
Counts RMSZ #|Z| > 2
17,23,23
1.23
1 (5%)
3,3,30.21
03,3,30.15
03,3,30.3703,3,30.150

In the following table, the Chirals column lists the number of chiral outliers, the number of chiral
centers 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.
Mol3

Type
HWH

ChainARes404

Link-Chirals-Torsions
1/6/6/6

Rings
0/2/2/2

All (3) bond length outliers are listed below:
Mol333ChainAAARes
404404404

Type
HWH
HWH
HWH

Atoms
C2-N1
C9-C10O1-C2Z
4.01
2.28
-2.11

Observed(Å)
1.45
1.39
1.18

Ideal(Å)
1.34
1.36
1.23

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5R7Z

All (1) bond angle outliers are listed below:
Mol
3

Chain
ARes
404

Type
HWH

Atoms
C11-C10-C9

Z
-2.80

Observed(o )120.14

Ideal(o )123.23

There are no chirality outliers.
All (1) torsion outliers are listed below:
Mol3

ChainARes
404

Type
HWH

Atoms
C3-C4-C5-C8

There are no ring outliers.
2 monomers are involved in 3 short contacts:
Mol22ChainAARes
402
405

TypeDMSDMSClashes12

Symm-Clashes
00

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 will
also 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 identified 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 identified 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-identified 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 find sufficientequivalents in the CSD to analyse the geometry.

Page 12Full wwPDB X-ray Structure Validation Report
Ligand HWH A 404

5.7

Bond lengths

Bond angles

Torsions

Rings

i
Other polymers ○There are no such residues in this entry.

5.8i
Polymer linkage issues ○There are no chain breaks in this entry.

5R7Z

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5R7Zi
Fit of model and data ○6.1

iProtein, DNA and RNA chains ○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.
MolChainAnalysed<RSRZ>

1A

304/306 (99%)-0.09#RSRZ>213 (4%) 35

32

OWAB(Å2 )Q<0.915, 23, 38, 56

10 (3%)All (13) RSRZ outliers are listed below:
Mol1111111111111Chain
A
A
A
A
A
A
A
A
A
A
A
A
A

Res
73[A]
221[A]
216[A]
303
49
154
190
41
191
165
192
302
294

Type
VAL
ASN
ASP
VAL
MET
TYR
THR
HIS
ALA
MET
GLN
GLY
PHE

RSRZ
15.3
8.6
7.4
3.8
3.5
3.1
3.1
3.1
2.7
2.7
2.2
2.2
2.1

6.2

i
Non-standard residues in protein, DNA, RNA chains ○There are no non-standard protein/DNA/RNA residues in this entry.

6.3

iCarbohydrates ○There are no monosaccharides in this entry.

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5R7Z

iLigands ○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
32222

TypeHWHDMSDMSDMS
DMS

ChainAAAAARes404405
403
401402

Atoms
16/16
4/4
4/4
4/4
4/4

RSCC
0.62
0.74
0.94
0.98
0.99

RSR
0.23
0.26
0.10
0.05
0.06

B-factors(Å2 )36,40,41,42
34,36,38,38
44,47,47,47
30,31,31,32
29,30,33,33

Q<0.9
16
4
000

The following is a graphical depiction of the model fit to experimental electron density of all
instances of the Ligand of Interest. In addition, ligands with molecular weight > 250 and outliers
as shown on the geometry validation Tables will also be included. Each fit is shown from different
orientation to approximate a three-dimensional view.

Electron density around HWH A 404:

2mFo -DFc (at 0.7 rmsd) in graymFo -DFc (at 3 rmsd) in purple (negative)
and green (positive)

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Full wwPDB X-ray Structure Validation Reporti
Other polymers ○There are no such residues in this entry.

5R7Z