iFull wwPDB X-ray Structure Validation Report ○Jun 25, 2024 – 12:50 AM EDTPDB ID : 6LU7Title : The crystal structure of COVID-19 main protease in complex with an inhibitor
N3Authors : Liu, X.; Zhang, B.; Jin, Z.; Yang, H.; Rao, Z.
Deposited on : 2020-01-26
Resolution : 2.16 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
Percentile statistics
Refmac
CCP4
Ideal geometry (proteins)
Ideal geometry (DNA, RNA)
Validation Pipeline (wwPDB-VP)

:::
:
:
:
:
:
:
:

4.02b-467
1.8.5 (274361), CSD as541be (2020)
1.132.37.1
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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6LU7i
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 2.16 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.

MetricRf reeClashscore
Ramachandran outliers
Sidechain outliers
RSRZ outliers

Whole archive(#Entries)
130704141614138981138945127900Similar resolution(#Entries, resolution range(Å))
1479 (2.16-2.16)
1585 (2.16-2.16)
1560 (2.16-2.16)
1559 (2.16-2.16)
1456 (2.16-2.16)

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

Length

1

A306

2

C6

Quality of chain

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6LU7iEntry composition ○There are 3 unique types of molecules in this entry. The entry contains 2500 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.
MolChainResidues

1A306

Atoms
TotalCN2367 1499 402

O444

S22ZeroOcc

AltConf

Trace

000

• Molecule 2 is a protein called N-[(5-METHYLISOXAZOL-3-YL)CARBONYL]ALANYL-LVALYL-N 1 -((1R,2Z)-4-(BENZYLOXY)-4-OXO-1-{[(3R)-2-OXOPYRROLIDIN-3-YL]ME
THYL}BUT-2-ENYL)-L-LEUCINAMIDE.
Mol

Chain

Residues

2C

6AtomsTotal C N
4935 6O
8ZeroOcc

AltConf

Trace

000

• Molecule 3 is water.
Mol

ChainResidues

3A

84

Atoms
Total O
8484

ZeroOcc

AltConf00Page 43Full wwPDB X-ray Structure Validation Report

6LU7iResidue-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

Y209

G179

C160
Y161
M162
H163
H164

•
•
D153
Y154
D155
C156

P132

Y126
Q127
C128

P122

L115

I106
Q107
P108

T98
P99
K100

•
•
D92
T93
A94
N95

V86

M82

•
•
V73
Q74
L75

L58
G278
R279

C300
S301
G302
V303
T304
F305
Q306

••
•
••

L50

E47

P39

T26
L27

E14
F223

S1I213•D229 •F230 •K236 •M276 •N277 •••Chain A:• Molecule 2: N-[(5-METHYLISOXAZOL-3-YL)CARBONYL]ALANYL-L-VALYL-N 1 -((1R,2Z)-4-(BENZYLOXY)-4-OXO-1-{[(3R)-2-OXOPYRROLIDIN-3-YL]METHYL}BUT-2-ENYL)-L-L
EUCINAMIDE

L4PJE50106

02J1

Chain C:Page 54

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6LU7i
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
97.93Å 79.48Å 51.80Å
90.00◦ 114.55◦ 90.00◦
27.81 – 2.16
42.31 – 2.16
99.5 (27.81-2.16)
99.6 (42.31-2.16)
0.19(Not available)
3.09 (at 2.16Å)
PHENIX 1.17.1_3660
0.202 , 0.235
0.204 , 0.235
998 reflections (5.13%)
34.7
0.488
0.34 , 45.9
< |L| > = 0.47, < L2 > = 0.29
No twinning to report.
0.94
2500
42.0Source
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 7.73% 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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iModel quality ○5.1

iStandard geometry ○Bond lengths and bond angles in the following residue types are not validated in this section: PJE,02J, 010
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).
MolChain12AllACAll

Bond lengths
RMSZ #|Z| >50.25
0/2420
1.59
0/19
0.29
0/2439Bond angles
RMSZ #|Z| >50.44
0/3289
0.65
0/25
0.44
0/3314

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.
Mol
123AllChainACAAll

Non-H2367
4984
2500

H(model)
0000H(added)
2313
4102354

Clashes235124

Symm-Clashes
0000The 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 (24) close contacts within the same asymmetric unit are listed below, sorted by their clashmagnitude.

Page 7Full wwPDB X-ray Structure Validation Report

Atom-1Atom-2

1:A:26:THR:H
1:A:106:ILE:HD12
1:A:115:LEU:HD11
1:A:100:LYS:HD3
1:A:26:THR:N
1:A:86:VAL:HG13
1:A:26:THR:H
1:A:126:TYR:HE2
1:A:27:LEU:HD13
1:A:108:PRO:HB3
1:A:213:ILE:HG21
1:A:106:ILE:C
1:A:127:GLN:NE2
1:A:95:ASN:HB3
1:A:277:ASN:OD1
1:A:106:ILE:HD12
1:A:58:LEU:HD22
1:A:26:THR:O
1:A:304:THR:HG23
1:A:106:ILE:HG23
1:A:14:GLU:HG2
1:A:209:TYR:O
2:C:4:LEU:HD23
1:A:162:MET:O

2:C:6:010:H4
1:A:106:ILE:C
1:A:122:PRO:HB3
1:A:156:CYS:HB2
2:C:6:010:H4
1:A:179:GLY:HA2
2:C:6:010:C4
1:A:128:CYS:HG
1:A:39:PRO:HD2
1:A:132:PRO:HA
1:A:300:CYS:HB3
1:A:106:ILE:CD1
3:A:408:HOH:O
1:A:98:THR:OG1
1:A:279:ARG:NH2
1:A:106:ILE:O
1:A:82:MET:HB22:C:6:010:H4
1:A:305:PHE:H
1:A:160:CYS:HB2
1:A:122:PRO:HG2
1:A:213:ILE:HG13
2:C:4:LEU:HA
1:A:164:HIS:HD2

Interatomic
distance (Å)
1.41
2.10
1.83
1.85
2.19
1.94
2.20
1.61
1.96
1.95
1.96
2.80
2.48
2.14
2.48
2.16
1.99
2.17
1.83
2.01
2.01
2.21
1.88
2.03

6LU7

Clash
overlap (Å)
0.85
0.71
0.61
0.59
0.54
0.49
0.48
0.48
0.48
0.48
0.47
0.47
0.47
0.47
0.46
0.45
0.45
0.44
0.43
0.42
0.42
0.41
0.41
0.41

There are no symmetry-related clashes.

5.3

i
Torsion angles ○

5.3.1

i
Protein backbone ○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

Favoured

AllowedOutliers

1

A

304/306 (99%)

295 (97%)

9 (3%)02C

3/6 (50%)

3 (100%)

0Percentiles
100

100

0100 100Continued on next page...

Page 8Full wwPDB X-ray Structure Validation Report

Continued from previous page...
Mol Chain
Analysed
Favoured

AllowedOutliers

All9 (3%)

0All

307/312 (98%)

298 (97%)

6LU7Percentiles
100100

There are no Ramachandran outliers to report.
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 similar
resolution.
The Analysed column shows the number of residues for which the sidechain conformation was
analysed, and the total number of residues.
MolChainAnalysed

RotamericOutliers

Percentiles

1A

263/263 (100%)

262 (100%)1 (0%)

9193

2C

2/2 (100%)

2 (100%)0100100All

All

265/265 (100%)

264 (100%)1 (0%)91

93

All (1) residues with a non-rotameric sidechain are listed below:
Mol
1Chain
ARes
305

Type
PHE

Sometimes sidechains can be flipped to improve hydrogen bonding and reduce clashes. All (1) suchsidechains are listed below:
Mol
1ChainARes
164

5.3.3iRNA ○TypeHIS

There are no RNA molecules in this entry.

5.4

iNon-standard residues in protein, DNA, RNA chains ○2 non-standard protein/DNA/RNA residues 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. The

Page 9Full wwPDB X-ray Structure Validation Report

6LU7

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).

2

Bond lengths
Counts RMSZ #|Z| > 2
6,8,9
2.81
3 (50%)

Bond angles
Counts RMSZ #|Z| > 2
4,10,122.65
2 (50%)

1,212,13,14

12,16,18

Mol

TypeChainResLink

202JC

12PJEC52.79

5 (41%)

1.84

3 (25%)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.
Mol22

Type02J
PJE

ChainCCRes
1
5

Link
2
1,2

Chirals-Torsions
0/0/2/4
1/7/18/19

Rings
0/1/1/1
0/1/1/1

All (8) bond length outliers are listed below:
Mol22222222Chain
CCCCCCCC

Res
51155551Type
PJE
02J02J
PJE
PJE
PJE
PJE
02J

Atoms
C29-N6CA-C
C6-C5O8-C29
C21-C
CA-C20
CA-N
C4-CA

Z
7.55
5.25
3.52
-3.04
3.02
2.44
-2.08
2.04

Observed(Å)
1.41
1.54
1.52
1.17
1.53
1.53
1.41
1.43

Ideal(Å)
1.33
1.48
1.48
1.23
1.44
1.50
1.48
1.39

All (5) bond angle outliers are listed below:
Mol22222Chain
CC
CC
CRes
15551Type02J
PJE
PJEPJE
02J

Atoms
O-C-CA
CA-C20-C21
C27-C26-C29
C28-N6-C29
C4-CA-N

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

Z-4.62
-3.25
2.62
-2.35
-2.23

Observed(o )119.84119.76106.28109.23105.92

Ideal(o )124.22124.41102.88113.84109.94

Page 10Mol
2

Full wwPDB X-ray Structure Validation Report
ChainCRes
5TypePJE

Atoms
O-C-C21-C20

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

5.5i
Carbohydrates ○There are no monosaccharides in this entry.

5.6

i
Ligand geometry ○There are no ligands in this entry.

5.7

iOther polymers ○There are no such residues in this entry.

5.8

iPolymer linkage issues ○There are no chain breaks in this entry.

6LU7

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6LU7

i
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>

1

A

306/306 (100%)0.51

19 (6%) 20

2C

3/6 (50%)

0.22

0 100

AllAll309/312 (99%)

0.51

19 (6%) 21#RSRZ>227100
28OWAB(Å2 )Q<0.923, 42, 62, 81039, 39, 41, 420

23, 42, 62, 81

0All (19) RSRZ outliers are listed below:
Mol111111111111111111
1Chain
A
A
A
A
A
A
A
A
A
A
A
A
A
A
A
A
A
A
A

Res
305
304
306
277
73
154
92
93
303
153
301
276
50
236
230
229
47
75
223

Type
PHE
THR
GLN
ASN
VAL
TYR
ASP
THR
VAL
ASP
SER
MET
LEU
LYS
PHE
ASP
GLU
LEU
PHE

RSRZ
8.0
6.4
5.0
4.4
4.0
4.0
3.7
3.6
3.6
2.9
2.9
2.5
2.3
2.3
2.3
2.1
2.1
2.0
2.06.2i
Non-standard residues in protein, DNA, RNA chains ○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,

Page 12Full wwPDB X-ray Structure Validation Report

6LU7

median, 95th percentile and maximum values of B factors of atoms in the group. The column
labelled ‘Q< 0.9’ lists the number of atoms with occupancy less than 0.9.
Mol22

TypePJE02JChainCCRes51

6.3

i
Carbohydrates ○Atoms
13/14
8/9

RSCC
0.79
0.84

There are no monosaccharides in this entry.

6.4i
Ligands ○There are no ligands in this entry.

6.5iOther polymers ○There are no such residues in this entry.

RSR
0.16
0.29

B-factors(Å2 )20,20,20,20
47,54,63,64Q<0.900