iFull wwPDB X-ray Structure Validation Report ○Jun 18, 2024 – 07:19 AM EDTPDB ID : 5R7Y
Title : PanDDA analysis group deposition – Crystal Structure of COVID-19 main
protease in complex with Z45617795
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 : 1.65 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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5R7Yi
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 1.65 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 ree
Clashscore
Ramachandran outliers
Sidechain outliers

Whole archive(#Entries)
130704141614138981138945

Similar resolution(#Entries, resolution range(Å))
1827 (1.66-1.66)
1931 (1.66-1.66)
1891 (1.66-1.66)
1891 (1.66-1.66)

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%MolChain

Length1A306

Quality of chain

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5R7Yi
Entry composition ○There are 5 unique types of molecules in this entry. The entry contains 2779 atoms, of which 0are 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

Chain

Residues

1A

304

Atoms
TotalCN
2363 1493 402

O446

S22ZeroOcc

AltConfTrace020• Molecule 2 is N-(2-phenylethyl)methanesulfonamide (three-letter code: JFM) (formula:C9 H13 NO2 S) (labeled as "Ligand of Interest" by depositor).

MolChainResidues

2A

1AtomsTotal C N O
139 1 2S1ZeroOcc

AltConf00• Molecule 3 is DIMETHYL SULFOXIDE (three-letter code: DMS) (formula: C2 H6 OS).

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Mol

ChainResidues

3A

13A

13A

13A

1

Atoms
Total C O
42 1
Total C O
42 1Total C O
42 1Total C O
42 1S1S
1S1S1ZeroOcc

AltConf00000000• Molecule 4 is CHLORIDE ION (three-letter code: CL) (formula: Cl).
Mol

Chain

Residues

4A

1AtomsTotal Cl
11

ZeroOcc

AltConf00

Atoms
Total O386 386

ZeroOcc

AltConf065• Molecule 5 is water.
Mol

Chain

Residues

5A

321

5R7Y

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5R7Yi
Residue-property plots ○These plots are drawn for all protein, RNA, DNA and oligosaccharide chains in the entry. The firstgraphic for a chain summarises the proportions of the various outlier classes displayed in the secondgraphic. The second graphic shows the sequence view annotated by issues in geometry. Residues
are color-coded according to the number of geometric quality criteria for which they contain atleast one outlier: green = 0, yellow = 1, orange = 2 and red = 3 or more. 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: 3C-like proteinase

N277
G278

Q273N274

S267

Y239

M235
K236

L227

N221
R222

T199
I200

R188

C160

V157

Y154

S144
C145

S121
P122

Y118

L115

G109
Q110

V104

Y101

A94
N95

V303
T304
PHE
GLN

H80
R298

L50
P293
F294

S46

L27

L286
L287
E288
D289
E290

W31

S1
R279

Chain A:

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5R7Yi
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 setWilson 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
112.46Å 52.73Å 44.30Å
90.00◦ 102.81◦ 90.00◦
54.83 – 1.65
54.83 – 1.65
98.8 (54.83-1.65)
98.9 (54.83-1.65)
0.11(Not available)
1.12 (at 1.65Å)REFMAC 5.8.0238
0.179 , 0.237
0.235 , 0.260
1501 reflections (4.97%)
19.70.262
0.32 , 61.2
< |L| > = 0.51, < L2 > = 0.34
No twinning to report.
0.94
2779
24.0Source
Depositor
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 9.34% 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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5R7Yi
Model quality ○5.1iStandard geometry ○Bond lengths and bond angles in the following residue types are not validated in this section: CL,DMS, JFM
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).
Mol

Chain

1A

Bond lengths
RMSZ#|Z| >50.73
1/2415 (0.0%)

Bond angles
RMSZ #|Z| >50.83
0/3283All (1) bond length outliers are listed below:
Mol
1Chain
ARes
290

Type
GLU

Atoms
CD-OE2Z
6.95

Observed(Å)
1.33

Ideal(Å)
1.25

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

5.2

iToo-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.
Mol
12345All

ChainAAAAAAll

Non-H2363
13161386
2779

H(model)
000000H(added)
2305
024002329

Clashes
330011633

Symm-Clashes
000000The all-atom clashscore is defined as the number of clashes found per 1000 atoms (includinghydrogen atoms). The all-atom clashscore for this structure is 7.

Page 8Full wwPDB X-ray Structure Validation Report

5R7YAll (33) close contacts within the same asymmetric unit are listed below, sorted by their clashmagnitude.
Atom-1Atom-2

1:A:221[A]:ASN:ND2
1:A:221[A]:ASN:HD21
1:A:110:GLN:HG3
1:A:294:PHE:CD2
1:A:221[A]:ASN:HD21
1:A:1:SER:OG
1:A:279:ARG:NH2
1:A:293:PRO:HB3
1:A:221[A]:ASN:ND2
1:A:115:LEU:HD11
1:A:288:GLU:OE1
1:A:109:GLY:HA2
1:A:236:LYS:NZ
1:A:273:GLN:NE2
1:A:118:TYR:CE1
1:A:298:ARG:HG3
1:A:110:GLN:NE2
1:A:50:LEU:O
1:A:222:ARG:NE
1:A:277:ASN:N
1:A:101:TYR:HA
1:A:80:HIS:NE2
1:A:235:MET:HE2
1:A:274:ASN:OD1
1:A:94:ALA:HB2
1:A:104:VAL:O
1:A:286:LEU:C
1:A:199:THR:HG21
1:A:298:ARG:NH1
1:A:121:SER:HA
1:A:227:LEU:HD23
1:A:31:TRP:CD2
1:A:145:CYS:HB2

1:A:267:SER:HA
1:A:267:SER:HA
5:A:1342[B]:HOH:O
5:A:1269:HOH:O
1:A:267:SER:CA
5:A:1101[A]:HOH:O
5:A:1106[A]:HOH:O
5:A:1138[B]:HOH:O
1:A:267:SER:CA
1:A:122:PRO:HB3
5:A:1104:HOH:O
1:A:200:ILE:HD13
5:A:1111:HOH:O
5:A:1103:HOH:O
1:A:144:SER:HB3
1:A:303:VAL:HB
5:A:1122:HOH:O
1:A:188:ARG:NE
5:A:1123[A]:HOH:O
5:A:1107[A]:HOH:O
1:A:157:VAL:O
5:A:1110:HOH:O
5:A:1415:HOH:O
5:A:1105:HOH:O
5:A:1191[B]:HOH:O
1:A:160:CYS:HA
1:A:286:LEU:HD12
1:A:239:TYR:CZ
5:A:1142[A]:HOH:O
1:A:122:PRO:HD3
1:A:227:LEU:HA
1:A:95:ASN:HB2
4:A:1006:CL:CL

There are no symmetry-related clashes.

Interatomic
distance (Å)
1.58
1.04
1.49
2.23
1.85
2.02
2.26
1.93
2.49
1.83
2.16
1.84
2.35
2.12
2.41
1.89
2.40
2.39
2.42
2.28
2.11
2.34
2.14
2.20
2.16
2.19
2.40
2.55
2.53
1.82
1.86
2.56
2.59

Clash
overlap (Å)
1.17
1.16
1.09
0.90
0.89
0.76
0.69
0.67
0.62
0.61
0.60
0.59
0.59
0.57
0.56
0.55
0.54
0.53
0.52
0.51
0.500.50
0.47
0.47
0.44
0.42
0.42
0.41
0.41
0.41
0.41
0.40
0.40

Page 9Full wwPDB X-ray Structure Validation Report

5.3i
Torsion angles ○

5.3.1

i
Protein backbone ○5R7Y

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.
MolChainAnalysed

FavouredAllowedOutliers

1A

304/306 (99%)

301 (99%)2 (1%)

1 (0%)

Percentiles
41

22All (1) Ramachandran outliers are listed below:
Mol
1Chain
ARes
154

TypeTYR

5.3.2

i
Protein 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 similar
resolution.
The Analysed column shows the number of residues for which the sidechain conformation wasanalysed, and the total number of residues.
MolChainAnalysed

RotamericOutliers

1A

263/263 (100%)

261 (99%)2 (1%)

Percentiles
81

70

All (2) residues with a non-rotameric sidechain are listed below:
Mol
11ChainAARes
2746

TypeLEU
SER

Sometimes sidechains can be flipped to improve hydrogen bonding and reduce clashes. All (6) suchsidechains are listed below:
Mol11
1Chain ResTypeA
19GLN
A
72
ASN
A
110
GLN
Continued on next page...

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5R7Y

Continued from previous page...
Mol Chain ResType1A
119
ASN
1A
228
ASN
1A
238
ASN5.3.3

iRNA ○

There are no RNA molecules in this entry.

5.4i
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.

5.6

i
Ligand geometry ○Of 6 ligands modelled in this entry, 1 is monoatomic - leaving 5 for Mogul analysis.
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. The
Link 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).
MolTypeChainRes

Link3
3
3
3
2

DMS
DMSDMSDMSJFMAAAAA

1002
1003
1005
10041001-

Bond lengths
Counts RMSZ #|Z| > 2
3,3,3
0.16
0
3,3,30.27
03,3,30.25
03,3,30.30
013,13,13
1.75
2 (15%)

Bond angles
Counts RMSZ #|Z| > 2
3,3,3
0.11
0
3,3,30.14
03,3,30.14
0
3,3,3
0.17
0
16,17,17
3.82
6 (37%)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.

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TypeJFM

Chain
A

Res
1001

Link-Chirals-Torsions
3/7/7/7

5R7Y

Rings
0/1/1/1

All (2) bond length outliers are listed below:
Mol
22Chain
AA

Res
1001
1001

Type
JFM
JFM

Atoms
S02-N05
C01-S02

Z
4.94
2.91

Observed(Å)
1.70
1.82

Ideal(Å)
1.60
1.75

All (6) bond angle outliers are listed below:
Mol222222Chain
A
A
A
A
A
A

Res
1001
1001
1001
1001
1001
1001

Type
JFM
JFM
JFM
JFM
JFM
JFM

Atoms
O04-S02-O03
C01-S02-N05
O04-S02-N05
O03-S02-C01
C06-C07-C08
O04-S02-C01

Z-13.16
5.15
3.36
2.42
-2.28
2.17

Observed(o )99.93
110.91112.11112.16107.59111.77

Ideal(o )118.85
107.76107.31108.28112.87108.28There are no chirality outliers.
All (3) torsion outliers are listed below:
Mol
22
2

Chain
A
A
A

Res
1001
1001
1001

Type
JFM
JFM
JFM

Atoms
C06-N05-S02-C01
C06-N05-S02-O04
N05-C06-C07-C08

There are no ring outliers.
No monomer is involved in short contacts.
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 JFM A 1001

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.

5R7Y

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5R7Yi
Fit of model and data ○iProtein, DNA and RNA chains ○Unable to reproduce the depositors R factor - this section is therefore empty.

6.2i
Non-standard residues in protein, DNA, RNA chains ○Unable to reproduce the depositors R factor - this section is therefore empty.

6.3

i
Carbohydrates ○Unable to reproduce the depositors R factor - this section is therefore empty.

6.4

i
Ligands ○Unable to reproduce the depositors R factor - this section is therefore empty.
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 JFM A 1001:

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

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Other polymers ○Unable to reproduce the depositors R factor - this section is therefore empty.

5R7Y