i
wwPDB X-ray Structure Validation Summary Report ○Nov 21, 2023 – 12:48 AM JST
PDB ID : 7E5O
Title : Crystal structure of SARS-CoV-2 RBD in complex with antibody NT-193
Authors : Kita, S.; Onodera, T.; Adachi, Y.; Moriayma, S.; Nomura, T.; Tadokoro, T.;
Anraku, Y.; Yumoto, K.; Tian, C.; Fukuhara, H.; Suzuki, T.; Tonouchi, K.;
Sasaki, J.; Sun, L.; Hashiguchi, T.; Takahashi, Y.; Maenaka, K.
Deposited on : 2021-02-19
Resolution : 2.80 Å(reported)
This is a wwPDB X-ray Structure Validation Summary 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
CCP4Ideal geometry (proteins)
Ideal geometry (DNA, RNA)
Validation Pipeline (wwPDB-VP)

:::
:::
:
:
:
:

4.02b-467
1.8.5 (274361), CSD as541be (2020)
1.13
2.36
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)
2.36

Page 2

1

wwPDB X-ray Structure Validation Summary Report

7E5Oi
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 2.80 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
RSRZ outliers

Whole archive(#Entries)
130704141614138981138945127900Similar resolution(#Entries, resolution range(Å))
3140 (2.80-2.80)3569 (2.80-2.80)
3498 (2.80-2.80)
3500 (2.80-2.80)
3078 (2.80-2.80)

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

H244

2

L214

3

A215

4

B2

Quality of chain

Page 3

2

wwPDB X-ray Structure Validation Summary Report

7E5Oi
Entry composition ○There are 5 unique types of molecules in this entry. The entry contains 4833 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 NT-193 Heavy chain.
MolChain

Residues

1H220

Atoms
TotalCN
1662 1056 273

O327

S6

ZeroOcc

AltConf

Trace

000

ZeroOcc

AltConf

Trace

000

ZeroOcc

AltConf

Trace

000

• Molecule 2 is a protein called NT-193 Light chain.
Mol

Chain

Residues

2L

213

Atoms
Total
CN
1631 1028 278

O319

S
6

• Molecule 3 is a protein called Spike protein S1.
MolChain

Residues

3A188

Atoms
Total CNO S
1495 958 248 281 8• Molecule 4 is an oligosaccharide called 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose.

MolChainResidues

4B2Total
28

Atoms
C N
16 2O
10ZeroOcc

AltConf

Trace

000

• Molecule 5 is water.
Mol

ChainResidues

5H5Atoms
ZeroOcc AltConf
Total O00
5
5
Continued on next page...

Page 4

wwPDB X-ray Structure Validation Summary Report

Continued from previous page...
Mol Chain Residues
AtomsTotal O5L666Total O5A666ZeroOcc

AltConf

0000

7E5O

Page 53wwPDB X-ray Structure Validation Summary Report

7E5OiResidue-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: NT-193 Heavy chain

C223
ASP
LYS
GLY
SER
SER
LEU
GLU
VAL
LEU
PHE
GLN
GLY
PRO
LEU
GLY
HIS

N204
V205

S184

Q178

V159
S160

L145

S135
K136
S137
THR
SER
GLY
G141

Y104L82

V67

L63

Y59

K43
G44
L45

Q39
P40

G27

L11HISHIS
HIS
HISHIS

E1•

Chain H:

• Molecule 2: NT-193 Light chain

E214
CYS

N211

A435

H199

D171
S172
T173
Y174

T430

K191

Q167

E406

K184

S160

R403

•
Y141
P142

L126

I107

Q91
H92

••D389 •L390 •

W97

L79
T376
F377

T75

F72

G67

S64

L48

K43

Q38
L39
K40

N32
Y33
L34

V20
T21

M5

A2

•

Chain L:• Molecule 3: Spike protein S1

•L517
LEU
HIS

E465

L461

F456

S443

N439

•N394

C391

V382
S383

•
C361
V362
A363
D364
Y365
S366
V367

N343

ALA
PRO
A522
T523
V524
C525
GLY
PRO
LYS
LYS
SER
THR
ASN
LEU
VAL
LYS
ASN

•

PRO
THR
GLU
SER
ILE
VAL
ARG
PHE
PRO
ASN
ILE
THR
N334
L335
C336
P337

•Chain A:• Molecule 4: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-gluc
opyranose

NAG1
NAG2

Chain B:

Page 64

wwPDB X-ray Structure Validation Summary Report

7E5O

iData 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
P 21 21 2184.07Å 106.89Å 148.07Å
90.00◦
90.00◦
90.00◦
45.10 – 2.80
49.30 – 2.80
99.9 (45.10-2.80)
100.0 (49.30-2.80)
0.21(Not available)
1.64 (at 2.81Å)
PHENIX 1.18_3845
0.226 , 0.256
0.226 , 0.257
1665 reflections (4.96%)
59.1
0.617
0.30 , 26.9
< |L| > = 0.50, < L2 > = 0.33
No twinning to report.
0.92
4833
64.0Source
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 5.11% 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.
12Page 7

5

wwPDB X-ray Structure Validation Summary Report

7E5O

iModel quality ○5.1

iStandard geometry ○Bond lengths and bond angles in the following residue types are not validated in this section:
NAG
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

123AllHLAAll

Bond lengths
RMSZ #|Z| >50.41
0/17070.39
0/16680.43
0/15350.41
0/4910Bond angles
RMSZ #|Z| >50.57
0/23320.54
0/22620.60
0/20860.57
0/6680

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
1234555All

ChainHLA
B
A
HL
AllNon-H
1662
1631
1495
28
6564833

H(model)
00000000H(added)
1615
1599
1411
250004650

Clashes111612100038

Symm-Clashes
00000000

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 4.

Page 8wwPDB X-ray Structure Validation Summary Report

7E5O

The worst 5 of 38 close contacts within the same asymmetric unit are listed below, sorted by theirclash magnitude.
Atom-1Atom-2

2:L:107:ILE:H
2:L:21:THR:HG22
2:L:5:MET:HE1
1:H:178:GLN:OE1
3:A:361:CYS:HB3

2:L:167:GLN:HE22
2:L:75:THR:HG23
2:L:91:GLN:HB3
1:H:184:SER:HB2
3:A:391:CYS:HB3

Interatomicdistance (Å)
1.31
1.77
1.78
1.98
1.85

Clashoverlap (Å)
0.79
0.66
0.65
0.62
0.59

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 entriesof 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

Percentiles

1

H

216/244 (88%)

209 (97%)

7 (3%)

01001002

L

211/214 (99%)

206 (98%)

5 (2%)

0100

100

3

A

184/215 (86%)

171 (93%)

11 (6%)

2 (1%)

1441

All

All

611/673 (91%)

586 (96%)

23 (4%)

2 (0%)4172

All (2) Ramachandran outliers are listed below:
Mol
33Chain
AARes
337
383

TypePRO
SER

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Page 9wwPDB X-ray Structure Validation Summary Report

7E5O

analysed, and the total number of residues.
MolChainAnalysed

RotamericOutliers

Percentiles

1

H

188/208 (90%)

187 (100%)1 (0%)

88

96

2

L

181/182 (100%)

178 (98%)

3 (2%)

60

87

3A

163/188 (87%)

161 (99%)2 (1%)

7192AllAll532/578 (92%)

526 (99%)

6 (1%)

7392

5 of 6 residues with a non-rotameric sidechain are listed below:
Mol
233
21ChainLA
A
L
H

Res
160
366
377
32
104

TypeSER
SER
PHE
ASN
TYR

Sometimes sidechains can be flipped to improve hydrogen bonding and reduce clashes. 5 of 6 suchsidechains are listed below:
Mol
223
11ChainL
L
A
H
H

Res
167
200
360
393

5.3.3

i
RNA ○TypeGLN
GLN
ASN
GLN
GLN

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 ○2 monosaccharides 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 10

wwPDB X-ray Structure Validation Summary Report

7E5O

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).

3,4

Bond lengths
Counts RMSZ #|Z| > 2
14,14,150.61
0Bond angles
Counts RMSZ #|Z| > 2
17,19,21
1.59
2 (11%)

4

14,14,15

17,19,21

Mol

TypeChainResLink4NAG

B

14NAG

B

20.56

01.08

1 (5%)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.
Mol
44Type
NAG
NAG

ChainB
B

Res
12

Link
3,44

Chirals-Torsions
1/6/23/26
0/6/23/26

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

There are no bond length outliers.
All (3) bond angle outliers are listed below:
Mol
44
4

ChainBBBRes
1
12Type
NAG
NAG
NAG

Atoms
O5-C1-C2
C1-O5-C5
C1-O5-C5

Z-4.043.79
3.28

Observed(o )104.90117.33116.63

Ideal(o )111.29112.19112.19There are no chirality outliers.
All (1) torsion outliers are listed below:
Mol
4ChainB

Res
1

TypeNAG

Atoms
C4-C5-C6-O6

There are no ring outliers.
1 monomer is involved in 1 short contact:
Mol
4Chain
B

Res
1

Type
NAG

Clashes
1Symm-Clashes
0The following is a two-dimensional graphical depiction of Mogul quality analysis of bond lengths,bond angles, torsion angles, and ring geometry for oligosaccharide.

Page 11

wwPDB X-ray Structure Validation Summary Report
Oligosaccharide Chain B

5.6

Bond lengths

Bond angles

Torsions

Rings

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

5.7

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

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

7E5O

Page 126

wwPDB X-ray Structure Validation Summary Report

7E5O

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>OWAB(Å2 )Q<0.91H

220/244 (90%)-0.24

1 (0%) 91

8846, 59, 87, 12702L

213/214 (99%)-0.25

2 (0%) 84

80

44, 62, 80, 92

03A

188/215 (87%)-0.02

9 (4%) 30

2145, 61, 118, 151

0All

All

621/673 (92%)-0.18

12 (1%) 66

59

44, 61, 98, 151

0#RSRZ>2

The worst 5 of 12 RSRZ outliers are listed below:
Mol133
33Chain
H
A
A
AA

Res
27
335
390
389
524

Type
GLYLEU
LEU
ASP
VAL

RSRZ
3.8
3.2
3.2
3.1
2.9

6.2i
Non-standard residues in protein, DNA, RNA chains ○There are no non-standard protein/DNA/RNA residues in this entry.

6.3iCarbohydrates ○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 column
labelled ‘Q< 0.9’ lists the number of atoms with occupancy less than 0.9.
Mol
44TypeNAG
NAG

ChainBBRes21Atoms
14/15
14/15

RSCC
0.83
0.95

RSR0.280.16

B-factors(Å2 )86,106,115,118
71,80,87,90

Q<0.9
00

The following is a graphical depiction of the model fit to experimental electron density for oligosac-Page 13

wwPDB X-ray Structure Validation Summary Reportcharide. Each fit is shown from different orientation to approximate a three-dimensional view.

Electron density around Chain B:

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

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

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

7E5O