full wwpdb x-ray structure validation report o i · 1 a 108 leu cb-cg-cd2 -5.91 100.96 111.00 1 d...
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Full wwPDB X-ray Structure Validation Report iO
Aug 9, 2020 � 06:00 AM BST
PDB ID : 1FUJTitle : PR3 (MYELOBLASTIN)
Authors : Fujinaga, M.; Chernaia, M.M.; Halenbeck, R.; Koths, K.; James, M.N.G.Deposited on : 1996-01-25Resolution : 2.20 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 : 2.13.1
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) : 2.13.1
Page 2 Full wwPDB X-ray Structure Validation Report 1FUJ
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 2.20 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))
Clashscore 141614 5594 (2.20-2.20)Ramachandran outliers 138981 5503 (2.20-2.20)
Sidechain outliers 138945 5504 (2.20-2.20)
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 <=5%
Mol Chain Length Quality of chain
1 A 221
1 B 221
1 C 221
1 D 221
2 E 2
2 F 2
2 G 2
2 H 2
Page 3 Full wwPDB X-ray Structure Validation Report 1FUJ
2 Entry composition iO
There are 3 unique types of molecules in this entry. The entry contains 7174 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 PR3.
Mol Chain Residues Atoms ZeroOcc AltConf Trace
1 A 221Total C N O S1708 1083 311 303 11
0 0 0
1 B 221Total C N O S1708 1083 311 303 11
0 0 0
1 C 221Total C N O S1708 1083 311 303 11
0 0 0
1 D 221Total C N O S1708 1083 311 303 11
0 0 0
There are 4 discrepancies between the modelled and reference sequences:
Chain Residue Modelled Actual Comment ReferenceA 103 ILE VAL con�ict UNP P24158B 103 ILE VAL con�ict UNP P24158C 103 ILE VAL con�ict UNP P24158D 103 ILE VAL con�ict UNP P24158
� Molecule 2 is an oligosaccharide called alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose.
Mol Chain Residues Atoms ZeroOcc AltConf Trace
2 E 2Total C N O24 14 1 9
0 0 0
2 F 2Total C N O24 14 1 9
0 0 0
2 G 2Total C N O24 14 1 9
0 0 0
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Page 4 Full wwPDB X-ray Structure Validation Report 1FUJ
Continued from previous page...
Mol Chain Residues Atoms ZeroOcc AltConf Trace
2 H 2Total C N O24 14 1 9
0 0 0
� Molecule 3 is water.
Mol Chain Residues Atoms ZeroOcc AltConf
3 A 74Total O74 74
0 0
3 B 48Total O48 48
0 0
3 C 67Total O67 67
0 0
3 D 57Total O57 57
0 0
Page 5 Full wwPDB X-ray Structure Validation Report 1FUJ
3 Residue-property plots iO
These plots are drawn for all protein, RNA, DNA and oligosaccharide chains in the entry. The �rstgraphic 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. Residuesare 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: PR3
Chain A:
I16
E21
R27
P28
Y29
M30
M35
R36
S39
I47
H48
P49
S50
F51
A56
H57
C58
L59
R60
D61
L63C
V64
N65
L68
H71
R74
T75
Q76
E77
Q80
Q81
H82
F83
S84
V85
L90
N92
N93
Y94
D95
L100
N101
L104
L105
I106
Q107
L108
L114
S117
P124
P131
T134
L137
A138
M139
G142
R143
D148
P150
P151
N159
F165
F166
C168
R177
P178
H179
N180
I181
R186A
R186B
G193
D194
S195
G196
G197
P198
G207
I208
I209
D213
T221
R222
L223
T229
Y234
I238
R239
L242
R243
• Molecule 1: PR3
Chain B:
I16
G19
R27
P28
Y29
M30
Q34
M35
R36
S39
H40
T45
L46
I47
H48
P49
S50
F51
H57
C58
L59
R60
D61
I62
P63
L63C
V64
N65
V66
V67
L68
G69
A70
H71
N72
Q76
E77
Q80
Q81
H82
F83
S84
V85
A86
Q87
V88
F89
L90
N92
N93
Y94
D95
A96
L100
N101
L105
L108
S109
A112
N113
L114
V118
L137
A138
M139
V144
H147
D148
P150
P151
A152
Q153
V154
L155
Q156
E157
L158
T161
F166
C168
R177
P178
H179
N180
I181
C182
T183
F184
V185
P186
R186A
R186B
K187
A188
D194
S195
G196
G197
P198
L199
I200
C201
D202
G207
I208
D213
A220A
T221
R222
P225
F228
T229
R230
L233
Y234
I238
R239
L242
R243
• Molecule 1: PR3
Chain C:
I16
H20
Q23
Q34
M35
R36
G38
N38A
S39
T45
P49
L53
A56
H57
C58
L59
R60
D61
I62
P63
Q63A
V64
N65
G69
A70
H71
N72
V73
R74
T75
Q76
E77
Q80
Q81
H82
V85
L90
N92
N93
Y94
D95
K99
L100
N101
D102
I103
L104
L105
L114
S117
Q125
Q135
C136
L137
R143
V144
G145
A146
H147
D148
P150
P151
A152
Q153
V154
E157
L158
F165
R177
R186A
R186B
K187
I190
S195
G196
G197
P198
L199
I200
G207
I208
I209
Q210
G211
I212
D213
S214
A220A
L223
F224
P225
D226
T229
A232
L233
Y234
V235
I238
R239
S240
T241
L242
R243
Page 6 Full wwPDB X-ray Structure Validation Report 1FUJ
• Molecule 1: PR3
Chain D:
I16
V17
G18
G19
Q23
R27
P28
Y29
Q34
M35
R36
H40
T45
L46
I47
H48
P49
S50
F51
V52
A56
H57
C58
L59
R60
D61
I62
P63
Q63A
R63B
L63C
V66
H71
T75
Q76
E77
P78
T79
Q80
F83
V88
N93
N101
L104
L105
I106
Q107
A112
N113
L114
A119
L123
Q135
C136
L137
G142
R143
V144
G145
P151
A152
Q153
V154
L158
F165
F166
C168
R177
P178
H179
C182
R186A
R186B
K187
C191
F192
G193
D194
S195
G196
G197
P198
L199
I200
I208
I209
I212
I217
W218
G219
R222
L223
F224
P225
D226
F227
R230
V231
A232
L233
Y234
V235
I238
R239
S240
T241
L242
R243
• Molecule 2: alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose
Chain E:
NAG1
FUC2
• Molecule 2: alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose
Chain F:
NAG1
FUC2
• Molecule 2: alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose
Chain G:
NAG1
FUC2
• Molecule 2: alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose
Chain H:
NAG1
FUC2
Page 7 Full wwPDB X-ray Structure Validation Report 1FUJ
4 Data and re�nement statistics iO
Property Value SourceSpace group P 1 21 1 DepositorCell constantsa, b, c, α, β, γ
85.60Å 54.07Å 113.51Å90.00◦ 90.69◦ 90.00◦
Depositor
Resolution (Å)10.00 � 2.2068.74 � 1.98
DepositorEDS
% Data completeness(in resolution range)
93.4 (10.00-2.20)89.6 (68.74-1.98)
DepositorEDS
Rmerge (Not available) DepositorRsym (Not available) Depositor
< I/σ(I) > 1 1.22 (at 1.98Å) XtriageRe�nement program TNT Depositor
R, Rfree(Not available) , (Not available)
0.179 , (Not available)DepositorDCC
Rfree test set No test �ags present. wwPDB-VPWilson B-factor (Å2) 26.4 Xtriage
Anisotropy 0.716 XtriageBulk solvent ksol(e/Å3), Bsol(Å2) 0.34 , 124.6 EDS
L-test for twinning2 < |L| > = 0.48, < L2 > = 0.31 XtriageEstimated twinning fraction 0.043 for h,-k,-l Xtriage
Fo,Fc correlation 0.96 EDSTotal number of atoms 7174 wwPDB-VP
Average B, all atoms (Å2) 33.0 wwPDB-VP
Xtriage's analysis on translational NCS is as follows: The largest o�-origin peak in the Patterson
function is 4.50% 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.
Page 8 Full wwPDB X-ray Structure Validation Report 1FUJ
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:NAG, FUC
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 angles
RMSZ #|Z| >5 RMSZ #|Z| >51 A 0.97 2/1754 (0.1%) 1.09 6/2393 (0.3%)1 B 0.92 0/1754 1.08 3/2393 (0.1%)1 C 0.90 0/1754 1.01 1/2393 (0.0%)1 D 0.91 0/1754 1.03 6/2393 (0.3%)All All 0.92 2/7016 (0.0%) 1.05 16/9572 (0.2%)
All (2) bond length outliers are listed below:
Mol Chain Res Type Atoms Z Observed(Å) Ideal(Å)1 A 195 SER CA-CB 5.68 1.61 1.521 A 195 SER CB-OG 5.40 1.49 1.42
All (16) bond angle outliers are listed below:
Mol Chain Res Type Atoms Z Observed(o) Ideal(o)1 A 90 LEU CA-CB-CG 7.78 133.19 115.301 A 63(C) LEU CA-CB-CG -6.91 99.41 115.301 A 208 ILE CG1-CB-CG2 -6.29 97.56 111.401 A 108 LEU CB-CG-CD2 -5.91 100.96 111.001 D 200 ILE CG1-CB-CG2 -5.83 98.56 111.401 A 181 ILE N-CA-C -5.41 96.39 111.001 B 200 ILE CG1-CB-CG2 -5.34 99.65 111.401 B 63(C) LEU CA-CB-CG 5.33 127.57 115.301 D 143 ARG NE-CZ-NH1 -5.28 117.66 120.301 D 137 LEU CB-CG-CD2 -5.27 102.04 111.001 C 226 ASP N-CA-C -5.13 97.16 111.001 D 194 ASP CB-CG-OD2 5.12 122.91 118.301 D 226 ASP N-CA-C -5.09 97.25 111.001 D 145 GLY N-CA-C -5.09 100.38 113.101 A 238 ILE CG1-CB-CG2 -5.07 100.24 111.40
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Page 9 Full wwPDB X-ray Structure Validation Report 1FUJ
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Mol Chain Res Type Atoms Z Observed(o) Ideal(o)1 B 181 ILE CG1-CB-CG2 -5.06 100.27 111.40
There are no chirality outliers.
There are no planarity outliers.
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.
Mol Chain Non-H H(model) H(added) Clashes Symm-Clashes1 A 1708 0 1672 54 01 B 1708 0 1672 69 01 C 1708 0 1672 59 01 D 1708 0 1672 70 02 E 24 0 22 1 02 F 24 0 22 2 02 G 24 0 22 1 02 H 24 0 22 1 03 A 74 0 0 3 03 B 48 0 0 3 03 C 67 0 0 2 03 D 57 0 0 2 0All All 7174 0 6776 249 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 18.
All (249) close contacts within the same asymmetric unit are listed below, sorted by their clashmagnitude.
Atom-1 Atom-2Interatomicdistance (Å)
Clashoverlap (Å)
1:D:49:PRO:HG3 1:D:114:LEU:HD11 1.46 0.981:C:59:LEU:HD22 1:C:62:ILE:HD11 1.51 0.921:D:63:PRO:HD2 1:D:63(C):LEU:HD12 1.53 0.911:B:230:ARG:HG2 1:B:233:LEU:HD13 1.56 0.861:D:123:LEU:HD23 1:D:209:ILE:HD11 1.60 0.831:B:77:GLU:HB2 1:B:80:GLN:HG3 1.63 0.811:C:95:ASP:HB3 1:C:100:LEU:HB2 1.62 0.81
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Page 10 Full wwPDB X-ray Structure Validation Report 1FUJ
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Atom-1 Atom-2Interatomicdistance (Å)
Clashoverlap (Å)
1:A:143:ARG:HA 1:A:151:PRO:HA 1.63 0.791:A:90:LEU:HD22 1:A:104:LEU:HG 1.69 0.741:C:49:PRO:HG3 1:C:114:LEU:HD11 1.69 0.741:B:63:PRO:HB2 1:B:63(C):LEU:HD13 1.69 0.731:C:90:LEU:HG 1:C:104:LEU:HD12 1.70 0.721:D:77:GLU:HB2 1:D:80:GLN:NE2 2.05 0.711:D:105:LEU:HD23 1:D:241:THR:HG21 1.72 0.711:C:57:HIS:CE1 1:C:195:SER:HB3 2.26 0.701:B:166:PHE:HD2 1:C:165:PHE:HE1 1.39 0.701:D:101:ASN:H 1:D:179:HIS:HE1 1.40 0.701:A:30:MET:SD 1:A:139:MET:HE3 2.32 0.691:B:222:ARG:HG2 1:B:222:ARG:HH11 1.57 0.691:A:198:PRO:HB3 1:A:209:ILE:HD12 1.73 0.691:C:65:ASN:HD21 1:C:82:HIS:HB3 1.58 0.671:D:49:PRO:HG3 1:D:114:LEU:CD1 2.23 0.671:B:86:ALA:HB2 1:B:109:SER:HA 1.76 0.661:B:184:PHE:CE2 1:B:186:PRO:HA 2.31 0.651:D:77:GLU:HB2 1:D:80:GLN:HE21 1.57 0.651:D:123:LEU:CD2 1:D:209:ILE:HD11 2.26 0.651:C:190:ILE:HD12 1:C:213:ASP:HB3 1.78 0.651:C:59:LEU:CD2 1:C:62:ILE:HD11 2.27 0.641:C:187:LYS:HG2 1:C:220(A):ALA:HB1 1.79 0.631:A:101:ASN:H 1:A:179:HIS:HE1 1.46 0.621:D:51:PHE:CE2 1:D:107:GLN:HG3 2.34 0.621:B:62:ILE:HD13 1:B:64:VAL:HG22 1.82 0.621:D:105:LEU:HD23 1:D:241:THR:CG2 2.29 0.621:B:49:PRO:HG3 1:B:114:LEU:HD11 1.81 0.621:D:77:GLU:HB2 1:D:80:GLN:HG3 1.82 0.621:A:137:LEU:HD12 1:A:159:ASN:HA 1.82 0.621:A:101:ASN:H 1:A:179:HIS:CE1 2.18 0.611:C:74:ARG:HD2 1:C:153:GLN:NE2 2.16 0.601:D:23:GLN:HA 1:D:23:GLN:NE2 2.16 0.601:B:65:ASN:HD21 1:B:82:HIS:HB3 1.65 0.601:D:144:VAL:HG13 1:D:152:ALA:HB2 1.82 0.601:D:101:ASN:H 1:D:179:HIS:CE1 2.19 0.601:A:27:ARG:HB3 1:A:139:MET:HE1 1.84 0.591:C:53:LEU:HD23 1:C:209:ILE:HD13 1.84 0.591:B:230:ARG:CG 1:B:233:LEU:HD13 2.31 0.591:A:239:ARG:HD3 3:A:301:HOH:O 2.03 0.591:C:143:ARG:HA 1:C:151:PRO:HA 1.84 0.591:C:239:ARG:O 1:C:243:ARG:HD2 2.03 0.59
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Page 11 Full wwPDB X-ray Structure Validation Report 1FUJ
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Atom-1 Atom-2Interatomicdistance (Å)
Clashoverlap (Å)
1:A:186(A):ARG:HG3 1:A:186(B):ARG:HD3 1.85 0.581:D:59:LEU:HD22 1:D:104:LEU:HD21 1.86 0.581:D:135:GLN:HA 1:D:135:GLN:HE21 1.67 0.581:A:48:HIS:HB3 1:A:51:PHE:HB2 1.84 0.581:D:238:ILE:O 1:D:242:LEU:HD13 2.04 0.58
1:D:52:VAL:HG21 1:D:66:VAL:HG11 1.84 0.581:D:144:VAL:CG1 1:D:152:ALA:HB2 2.34 0.581:A:16:ILE:N 1:A:194:ASP:OD2 2.37 0.58
1:C:62:ILE:HD13 1:C:64:VAL:CG2 2.34 0.571:C:63(A):GLN:NE2 1:C:85:VAL:HG12 2.19 0.571:C:95:ASP:CB 1:C:100:LEU:HB2 2.35 0.57
1:A:186(A):ARG:CG 1:A:186(B):ARG:HD3 2.34 0.571:D:23:GLN:HA 1:D:23:GLN:HE21 1.69 0.571:D:45:THR:OG1 1:D:198:PRO:HB3 2.04 0.571:C:75:THR:HG22 1:C:76:GLN:H 1.70 0.561:B:200:ILE:HD13 2:F:2:FUC:H62 1.87 0.561:C:77:GLU:HB2 1:C:80:GLN:HG3 1.88 0.561:C:59:LEU:HD22 1:C:62:ILE:CD1 2.31 0.561:D:19:GLY:HA2 1:D:158:LEU:HD13 1.86 0.561:B:63:PRO:HB2 1:B:63(C):LEU:CD1 2.36 0.561:D:47:ILE:HG12 1:D:123:LEU:HD21 1.87 0.561:A:51:PHE:CD2 1:A:242:LEU:HD22 2.42 0.551:B:16:ILE:N 1:B:194:ASP:OD2 2.40 0.55
1:D:71:HIS:CD2 1:D:154:VAL:HG22 2.41 0.551:A:234:TYR:O 1:A:238:ILE:HG13 2.05 0.551:D:28:PRO:HG2 1:D:119:ALA:HB3 1.89 0.551:B:93:ASN:N 1:B:93:ASN:OD1 2.40 0.55
1:C:187:LYS:HE3 1:C:220(A):ALA:O 2.06 0.541:B:197:GLY:HA3 3:B:247:HOH:O 2.08 0.541:C:232:ALA:HA 1:C:235:VAL:HG23 1.90 0.541:D:57:HIS:NE2 1:D:195:SER:HB3 2.22 0.541:A:124:PRO:HD3 1:A:209:ILE:O 2.07 0.541:B:27:ARG:HG2 1:B:139:MET:SD 2.48 0.541:C:207:GLY:H 2:G:2:FUC:HO4 1.56 0.54
1:A:197:GLY:HA3 3:A:248:HOH:O 2.09 0.531:B:95:ASP:HB3 1:B:100:LEU:HB2 1.88 0.531:D:77:GLU:CB 1:D:80:GLN:HG3 2.38 0.53
1:A:229:THR:HG23 3:A:258:HOH:O 2.09 0.531:C:38(A):ASN:HB3 1:C:39:SER:HB3 1.90 0.531:D:34:GLN:HG2 1:D:40:HIS:HA 1.89 0.531:A:57:HIS:CE1 1:A:195:SER:HB3 2.43 0.53
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Page 12 Full wwPDB X-ray Structure Validation Report 1FUJ
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Atom-1 Atom-2Interatomicdistance (Å)
Clashoverlap (Å)
1:C:73:VAL:HG22 1:C:153:GLN:O 2.08 0.531:A:168:CYS:SG 1:A:177:ARG:N 2.81 0.531:D:187:LYS:HA 1:D:222:ARG:HD2 1.90 0.53
1:C:137:LEU:HD12 1:C:158:LEU:O 2.09 0.521:A:58:CYS:C 1:A:59:LEU:HD12 2.30 0.52
1:A:35:MET:HB2 1:A:39:SER:OG 2.09 0.521:B:94:TYR:CE2 1:B:96:ALA:HB2 2.44 0.521:D:60:ARG:O 1:D:62:ILE:HD12 2.09 0.52
1:C:210:GLN:NE2 3:C:306:HOH:O 2.40 0.521:C:36:ARG:HH11 1:C:36:ARG:HB3 1.73 0.521:A:47:ILE:HD12 1:A:242:LEU:HD11 1.92 0.521:D:16:ILE:HD13 1:D:194:ASP:OD2 2.09 0.521:D:19:GLY:CA 1:D:158:LEU:HD13 2.40 0.511:B:200:ILE:HD12 1:B:200:ILE:O 2.11 0.511:B:27:ARG:HD3 1:B:157:GLU:OE1 2.11 0.511:B:34:GLN:HG2 1:B:40:HIS:HA 1.93 0.511:D:59:LEU:HD22 1:D:104:LEU:CD2 2.41 0.511:A:85:VAL:HG13 1:A:106:ILE:HG23 1.91 0.511:D:234:TYR:O 1:D:238:ILE:HG13 2.11 0.51
1:A:186(A):ARG:HG3 1:A:186(B):ARG:N 2.25 0.511:B:183:THR:HG1 1:B:228:PHE:HE1 1.59 0.511:B:45:THR:OG1 1:B:198:PRO:HG3 2.11 0.501:B:180:ASN:O 1:B:230:ARG:NH1 2.45 0.50
1:D:104:LEU:HD23 1:D:106:ILE:HG13 1.92 0.501:A:49:PRO:HG3 1:A:114:LEU:HD11 1.93 0.501:C:71:HIS:O 1:C:154:VAL:HA 2.12 0.50
1:C:186(B):ARG:HH11 1:C:186(B):ARG:HG2 1.77 0.501:D:59:LEU:CD2 1:D:88:VAL:HG11 2.41 0.501:D:57:HIS:CE1 1:D:195:SER:HB3 2.47 0.491:C:103:ILE:HD13 1:C:234:TYR:CD2 2.47 0.491:A:65:ASN:HD21 1:A:82:HIS:HB3 1.77 0.491:C:213:ASP:OD1 1:C:213:ASP:N 2.44 0.491:D:16:ILE:N 1:D:194:ASP:OD2 2.45 0.49
1:C:105:LEU:HD11 1:C:238:ILE:HG23 1.93 0.491:A:131:PRO:O 1:A:134:THR:HG23 2.13 0.491:B:144:VAL:CG2 1:B:148:ASP:HB3 2.42 0.491:C:58:CYS:C 1:C:59:LEU:HD23 2.33 0.49
1:A:36:ARG:HG2 1:A:65:ASN:HB2 1.94 0.491:B:182:CYS:HB3 1:B:225:PRO:HB2 1.94 0.491:B:200:ILE:CD1 2:F:2:FUC:H62 2.43 0.491:C:197:GLY:HA3 3:C:264:HOH:O 2.12 0.49
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Atom-1 Atom-2Interatomicdistance (Å)
Clashoverlap (Å)
1:A:29:TYR:HE1 1:A:139:MET:HE2 1.78 0.481:D:59:LEU:HD23 1:D:88:VAL:HG11 1.95 0.481:A:90:LEU:HD22 1:A:104:LEU:CG 2.40 0.481:B:36:ARG:NH1 1:B:84:SER:HB3 2.28 0.481:B:67:VAL:HG22 1:B:82:HIS:ND1 2.29 0.481:B:51:PHE:CD2 1:B:242:LEU:HD22 2.48 0.48
1:C:38(A):ASN:HB3 1:C:39:SER:CB 2.43 0.481:D:200:ILE:O 2:H:2:FUC:H4 2.13 0.481:B:48:HIS:HB3 1:B:51:PHE:HB2 1.95 0.481:B:70:ALA:HA 1:B:77:GLU:OE1 2.14 0.471:B:71:HIS:O 1:B:154:VAL:HA 2.14 0.47
1:B:89:PHE:HB2 1:B:105:LEU:HB2 1.96 0.471:D:56:ALA:HA 1:D:104:LEU:HD13 1.97 0.471:A:68:LEU:HD12 1:A:83:PHE:CE1 2.49 0.471:B:222:ARG:NH1 1:B:222:ARG:HG2 2.27 0.471:C:211:GLY:HA2 1:C:229:THR:O 2.14 0.471:D:19:GLY:HA2 1:D:158:LEU:CD1 2.44 0.471:B:83:PHE:CZ 1:B:112:ALA:HA 2.49 0.471:B:230:ARG:O 1:B:233:LEU:HB2 2.15 0.471:A:21:GLU:OE2 1:A:71:HIS:NE2 2.40 0.471:C:69:GLY:HA2 1:C:117:SER:O 2.14 0.471:B:59:LEU:HG 1:B:62:ILE:HD11 1.97 0.47
1:D:212:ILE:HD12 1:D:231:VAL:HG22 1.97 0.471:A:165:PHE:CZ 1:D:165:PHE:HB2 2.51 0.461:D:197:GLY:HA3 3:D:248:HOH:O 2.16 0.461:A:51:PHE:CE1 1:A:107:GLN:HB2 2.50 0.461:A:57:HIS:NE2 1:A:195:SER:HB3 2.31 0.461:A:27:ARG:O 1:A:30:MET:HB2 2.14 0.46
1:D:45:THR:HG22 1:D:47:ILE:CD1 2.46 0.461:A:77:GLU:HB2 1:A:80:GLN:HG3 1.97 0.461:B:27:ARG:HG2 1:B:139:MET:CE 2.45 0.461:B:68:LEU:O 1:B:80:GLN:HA 2.15 0.46
1:A:186(B):ARG:H 1:A:186(B):ARG:HG2 1.45 0.461:B:187:LYS:HD2 1:B:220(A):ALA:O 2.15 0.461:C:45:THR:OG1 1:C:198:PRO:HB3 2.15 0.461:C:57:HIS:NE2 1:C:195:SER:HB3 2.30 0.461:D:182:CYS:HB3 1:D:225:PRO:HB2 1.97 0.461:D:17:VAL:HG23 1:D:191:CYS:HB2 1.97 0.461:D:83:PHE:CZ 1:D:112:ALA:HA 2.51 0.461:C:59:LEU:N 1:C:59:LEU:HD23 2.31 0.45
1:B:184:PHE:HE2 1:B:186:PRO:HA 1.81 0.45Continued on next page...
Page 14 Full wwPDB X-ray Structure Validation Report 1FUJ
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Atom-1 Atom-2Interatomicdistance (Å)
Clashoverlap (Å)
1:C:187:LYS:CG 1:C:220(A):ALA:HB1 2.44 0.451:D:208:ILE:HD13 3:D:295:HOH:O 2.16 0.451:A:56:ALA:HA 1:A:104:LEU:HB2 1.99 0.451:C:212:ILE:HB 1:C:229:THR:HB 1.99 0.451:A:101:ASN:ND2 1:A:234:TYR:OH 2.44 0.451:B:202:ASP:O 1:B:208:ILE:HD12 2.17 0.451:A:35:MET:HB3 1:A:35:MET:HE3 1.59 0.45
1:C:186(B):ARG:NH1 1:C:186(B):ARG:HG2 2.32 0.451:C:61:ASP:N 1:C:61:ASP:OD1 2.50 0.45
1:B:101:ASN:HA 1:B:234:TYR:OH 2.17 0.451:B:83:PHE:CB 1:B:108:LEU:HD22 2.46 0.451:B:72:ASN:HA 1:B:153:GLN:O 2.17 0.451:C:74:ARG:HD2 1:C:153:GLN:HE21 1.82 0.451:A:95:ASP:HB3 1:A:100:LEU:HB2 1.99 0.441:A:198:PRO:CB 1:A:209:ILE:HD12 2.45 0.441:C:56:ALA:N 1:C:102:ASP:OD1 2.50 0.441:D:51:PHE:CZ 1:D:107:GLN:HG3 2.52 0.441:B:100:LEU:HA 1:B:100:LEU:HD23 1.76 0.441:B:19:GLY:HA2 1:B:158:LEU:HD13 2.00 0.441:B:57:HIS:NE2 1:B:195:SER:HB3 2.33 0.441:B:83:PHE:HB2 1:B:108:LEU:HD22 2.00 0.441:D:61:ASP:O 1:D:62:ILE:HG13 2.17 0.44
1:D:105:LEU:HD12 1:D:105:LEU:HA 1.68 0.441:B:234:TYR:O 1:B:238:ILE:HG13 2.18 0.441:B:77:GLU:HB2 1:B:80:GLN:CG 2.41 0.441:C:223:LEU:HD13 1:C:224:PHE:CZ 2.53 0.441:D:230:ARG:HD2 1:D:233:LEU:HD21 1.99 0.44
1:A:186(A):ARG:HB2 1:A:186(A):ARG:HE 1.57 0.431:B:185:VAL:HG11 1:B:188:ALA:HB3 1.99 0.431:B:137:LEU:HB3 1:B:200:ILE:HD11 2.00 0.431:C:95:ASP:O 1:C:99:LYS:N 2.52 0.43
1:A:238:ILE:HD13 1:A:238:ILE:HG21 1.67 0.431:C:20:HIS:O 1:C:157:GLU:N 2.40 0.43
1:D:142:GLY:HA2 1:D:193:GLY:HA3 2.00 0.431:D:235:VAL:O 1:D:239:ARG:HG3 2.18 0.431:B:63:PRO:CB 1:B:63(C):LEU:HD13 2.45 0.43
1:B:137:LEU:HD12 1:B:137:LEU:HA 1.85 0.431:A:142:GLY:HA2 1:A:193:GLY:HA3 2.01 0.431:D:77:GLU:HA 1:D:78:PRO:HD3 1.82 0.431:A:75:THR:HG22 1:A:76:GLN:N 2.34 0.431:C:197:GLY:O 1:C:212:ILE:HA 2.19 0.43
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Atom-1 Atom-2Interatomicdistance (Å)
Clashoverlap (Å)
1:D:143:ARG:HB3 1:D:191:CYS:SG 2.59 0.431:B:113:ASN:HD22 1:B:113:ASN:HA 1.76 0.421:C:198:PRO:HB2 1:C:200:ILE:HD13 2.00 0.421:D:27:ARG:HB3 1:D:27:ARG:HE 1.70 0.421:D:62:ILE:HA 1:D:63:PRO:HD3 1.89 0.42
1:A:208:ILE:HG23 1:A:208:ILE:HD13 1.55 0.421:B:242:LEU:N 1:B:242:LEU:HD23 2.34 0.421:D:59:LEU:HA 1:D:59:LEU:HD12 1.76 0.421:A:100:LEU:HA 1:A:179:HIS:CE1 2.54 0.421:C:198:PRO:HB2 1:C:200:ILE:CD1 2.50 0.421:C:75:THR:HG22 1:C:76:GLN:N 2.34 0.421:D:182:CYS:HB3 1:D:225:PRO:CB 2.50 0.421:B:48:HIS:CG 1:B:49:PRO:HD2 2.55 0.411:C:223:LEU:HA 1:C:223:LEU:HD23 1.49 0.41
1:B:186(B):ARG:HB2 1:B:186(B):ARG:HE 1.68 0.411:C:36:ARG:HA 1:C:65:ASN:HB2 2.02 0.411:D:45:THR:HG21 1:D:209:ILE:HG21 2.01 0.411:C:94:TYR:HA 1:C:101:ASN:HB2 2.03 0.411:D:217:ILE:HD11 1:D:227:PHE:CE1 2.56 0.411:D:60:ARG:HA 1:D:60:ARG:HD2 1.65 0.411:B:179:HIS:HB2 3:B:273:HOH:O 2.19 0.411:D:83:PHE:HZ 1:D:112:ALA:HA 1.85 0.411:B:88:VAL:HA 1:B:105:LEU:O 2.20 0.411:D:217:ILE:O 1:D:219:GLY:N 2.45 0.411:A:68:LEU:O 1:A:80:GLN:HA 2.21 0.411:B:83:PHE:HZ 1:B:112:ALA:HA 1.85 0.411:C:16:ILE:O 1:C:144:VAL:HG12 2.20 0.411:A:142:GLY:N 1:A:194:ASP:OD1 2.51 0.41
1:A:208:ILE:HD12 1:A:208:ILE:HG21 1.74 0.401:B:114:LEU:HA 1:B:118:VAL:O 2.20 0.401:B:155:LEU:HD12 1:B:155:LEU:HA 1.84 0.401:D:52:VAL:HG21 1:D:66:VAL:CG1 2.49 0.401:A:207:GLY:N 2:E:2:FUC:O4 2.43 0.40
1:B:166:PHE:HD2 1:C:165:PHE:CE1 2.29 0.401:B:27:ARG:HG3 1:B:29:TYR:OH 2.21 0.401:D:29:TYR:HA 1:D:119:ALA:O 2.22 0.40
1:B:229:THR:HG23 3:B:291:HOH:O 2.22 0.40
There are no symmetry-related clashes.
Page 16 Full wwPDB X-ray Structure Validation Report 1FUJ
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.
Mol Chain Analysed Favoured Allowed Outliers Percentiles
1 A 219/221 (99%) 204 (93%) 14 (6%) 1 (0%) 29 31
1 B 219/221 (99%) 197 (90%) 20 (9%) 2 (1%) 17 16
1 C 219/221 (99%) 201 (92%) 17 (8%) 1 (0%) 29 31
1 D 219/221 (99%) 205 (94%) 13 (6%) 1 (0%) 29 31
All All 876/884 (99%) 807 (92%) 64 (7%) 5 (1%) 25 26
All (5) Ramachandran outliers are listed below:
Mol Chain Res Type1 B 151 PRO1 C 146 ALA1 D 151 PRO1 A 150 PRO1 B 39 SER
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 187/187 (100%) 166 (89%) 21 (11%) 6 5
1 B 187/187 (100%) 161 (86%) 26 (14%) 3 3
1 C 187/187 (100%) 162 (87%) 25 (13%) 4 3
1 D 187/187 (100%) 164 (88%) 23 (12%) 4 4
All All 748/748 (100%) 653 (87%) 95 (13%) 4 3
Page 17 Full wwPDB X-ray Structure Validation Report 1FUJ
All (95) residues with a non-rotameric sidechain are listed below:
Mol Chain Res Type1 A 30 MET1 A 35 MET1 A 60 ARG1 A 61 ASP1 A 63(C) LEU1 A 74 ARG1 A 81 GLN1 A 90 LEU1 A 92 ASN1 A 93 ASN1 A 117 SER1 A 143 ARG1 A 148 ASP1 A 177 ARG1 A 186(A) ARG1 A 186(B) ARG1 A 195 SER1 A 208 ILE1 A 213 ASP1 A 221 THR1 A 223 LEU1 B 27 ARG1 B 30 MET1 B 35 MET1 B 47 ILE1 B 50 SER1 B 60 ARG1 B 61 ASP1 B 63(C) LEU1 B 76 GLN1 B 80 GLN1 B 90 LEU1 B 93 ASN1 B 139 MET1 B 147 HIS1 B 161 THR1 B 166 PHE1 B 177 ARG1 B 181 ILE1 B 186(B) ARG1 B 187 LYS1 B 195 SER
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Mol Chain Res Type1 B 213 ASP1 B 221 THR1 B 222 ARG1 B 230 ARG1 B 239 ARG1 C 23 GLN1 C 34 GLN1 C 35 MET1 C 36 ARG1 C 38(A) ASN1 C 61 ASP1 C 75 THR1 C 76 GLN1 C 90 LEU1 C 92 ASN1 C 117 SER1 C 125 GLN1 C 135 GLN1 C 147 HIS1 C 148 ASP1 C 165 PHE1 C 177 ARG1 C 186(A) ARG1 C 195 SER1 C 213 ASP1 C 214 SER1 C 223 LEU1 C 240 SER1 C 242 LEU1 C 243 ARG1 D 16 ILE1 D 23 GLN1 D 27 ARG1 D 35 MET1 D 36 ARG1 D 47 ILE1 D 60 ARG1 D 63(B) ARG1 D 75 THR1 D 93 ASN1 D 104 LEU1 D 113 ASN
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Mol Chain Res Type1 D 135 GLN1 D 143 ARG1 D 154 VAL1 D 166 PHE1 D 177 ARG1 D 186(A) ARG1 D 186(B) ARG1 D 195 SER1 D 222 ARG1 D 224 PHE1 D 243 ARG
Some sidechains can be �ipped to improve hydrogen bonding and reduce clashes. All (29) suchsidechains are listed below:
Mol Chain Res Type1 A 40 HIS1 A 63(A) GLN1 A 65 ASN1 A 92 ASN1 A 93 ASN1 A 101 ASN1 A 153 GLN1 A 179 HIS1 A 210 GLN1 B 34 GLN1 B 65 ASN1 B 76 GLN1 B 80 GLN1 B 113 ASN1 B 210 GLN1 C 38(A) ASN1 C 63(A) GLN1 C 65 ASN1 C 210 GLN1 D 23 GLN1 D 48 HIS1 D 63(A) GLN1 D 80 GLN1 D 87 GLN1 D 101 ASN1 D 113 ASN1 D 135 GLN
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Mol Chain Res Type1 D 179 HIS1 D 210 GLN
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
8 monosaccharides are modelled in this entry.
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| > 2
2 NAG E 1 1,2 14,14,15 1.47 2 (14%) 17,19,21 1.95 6 (35%)
2 FUC E 2 2 10,10,11 0.63 0 14,14,16 2.61 9 (64%)
2 NAG F 1 1,2 14,14,15 1.33 2 (14%) 17,19,21 2.75 8 (47%)
2 FUC F 2 2 10,10,11 0.78 0 14,14,16 2.96 6 (42%)
2 NAG G 1 1,2 14,14,15 1.60 2 (14%) 17,19,21 1.65 4 (23%)
2 FUC G 2 2 10,10,11 0.85 0 14,14,16 1.31 3 (21%)
2 NAG H 1 1,2 14,14,15 1.65 3 (21%) 17,19,21 2.02 6 (35%)
2 FUC H 2 2 10,10,11 0.71 0 14,14,16 2.49 6 (42%)
In the following table, the Chirals column lists the number of chiral outliers, the number of chiralcenters analysed, the number of these observed in the model and the number de�ned in theChemical Component Dictionary. Similar counts are reported in the Torsion and Rings columns.'-' means no outliers of that kind were identi�ed.
Page 21 Full wwPDB X-ray Structure Validation Report 1FUJ
Mol Type Chain Res Link Chirals Torsions Rings2 NAG E 1 1,2 - 4/6/23/26 0/1/1/12 FUC E 2 2 - - 0/1/1/12 NAG F 1 1,2 - 2/6/23/26 0/1/1/12 FUC F 2 2 - - 0/1/1/12 NAG G 1 1,2 - 4/6/23/26 0/1/1/12 FUC G 2 2 - - 0/1/1/12 NAG H 1 1,2 - 4/6/23/26 0/1/1/12 FUC H 2 2 - - 0/1/1/1
All (9) bond length outliers are listed below:
Mol Chain Res Type Atoms Z Observed(Å) Ideal(Å)2 H 1 NAG C8-C7 4.53 1.60 1.502 G 1 NAG C8-C7 4.01 1.58 1.502 E 1 NAG C8-C7 3.87 1.58 1.502 F 1 NAG C8-C7 2.63 1.56 1.502 F 1 NAG O5-C1 -2.62 1.39 1.432 E 1 NAG O5-C1 -2.53 1.39 1.432 H 1 NAG O5-C1 -2.43 1.39 1.432 H 1 NAG O7-C7 2.12 1.28 1.232 G 1 NAG C2-N2 2.04 1.49 1.46
All (48) bond angle outliers are listed below:
Mol Chain Res Type Atoms Z Observed(o) Ideal(o)2 F 2 FUC O5-C1-C2 7.59 122.48 110.772 F 1 NAG O5-C5-C6 -6.12 97.61 107.202 H 2 FUC O5-C1-C2 5.98 120.00 110.772 E 2 FUC O5-C1-C2 5.87 119.84 110.772 F 2 FUC C1-C2-C3 -4.57 104.05 109.672 F 1 NAG C3-C4-C5 -4.50 102.21 110.242 G 1 NAG O5-C5-C6 -3.99 100.95 107.202 H 1 NAG C1-O5-C5 -3.74 107.12 112.192 E 2 FUC O4-C4-C3 3.71 118.92 110.352 E 1 NAG C4-C3-C2 3.70 116.44 111.022 F 1 NAG O4-C4-C5 3.63 118.32 109.302 F 1 NAG O7-C7-C8 3.60 128.75 122.062 H 1 NAG O5-C5-C6 -3.48 101.75 107.202 H 1 NAG C4-C3-C2 3.46 116.09 111.022 E 1 NAG O5-C5-C6 -3.45 101.80 107.202 F 2 FUC C3-C4-C5 3.33 114.95 109.772 H 1 NAG O4-C4-C5 3.30 117.48 109.30
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Mol Chain Res Type Atoms Z Observed(o) Ideal(o)2 F 2 FUC C6-C5-C4 -3.27 107.02 113.072 H 2 FUC O4-C4-C3 3.27 117.91 110.352 G 1 NAG C2-N2-C7 3.15 127.38 122.902 E 2 FUC O2-C2-C1 3.08 115.44 109.152 F 1 NAG C8-C7-N2 -3.07 110.91 116.102 G 1 NAG C1-C2-N2 2.91 115.45 110.492 E 2 FUC O5-C5-C6 2.88 113.52 107.332 E 1 NAG O4-C4-C5 2.86 116.40 109.302 F 1 NAG O4-C4-C3 -2.84 103.79 110.352 E 1 NAG C2-N2-C7 2.81 126.91 122.902 F 2 FUC O5-C5-C6 2.79 113.33 107.332 G 2 FUC C2-C3-C4 2.75 115.65 110.892 H 2 FUC C2-C3-C4 2.51 115.24 110.892 H 2 FUC O3-C3-C2 2.49 114.75 109.992 E 2 FUC C2-C3-C4 2.43 115.10 110.892 F 1 NAG C6-C5-C4 2.41 118.65 113.002 E 2 FUC C6-C5-C4 -2.37 108.69 113.072 G 1 NAG O4-C4-C5 2.36 115.16 109.302 E 1 NAG C1-C2-N2 -2.34 106.50 110.492 H 1 NAG C2-N2-C7 2.31 126.19 122.902 H 1 NAG C1-C2-N2 -2.25 106.65 110.492 E 2 FUC C3-C4-C5 2.22 113.23 109.772 E 2 FUC O3-C3-C2 2.21 114.22 109.992 H 2 FUC C1-C2-C3 -2.20 106.96 109.672 H 2 FUC O2-C2-C1 2.19 113.62 109.152 G 2 FUC C6-C5-C4 2.18 117.09 113.072 F 1 NAG C1-O5-C5 -2.15 109.28 112.192 G 2 FUC O4-C4-C3 2.15 115.32 110.352 E 2 FUC C1-C2-C3 -2.10 107.09 109.672 F 2 FUC O2-C2-C1 2.06 113.37 109.152 E 1 NAG C1-O5-C5 -2.03 109.44 112.19
There are no chirality outliers.
All (14) torsion outliers are listed below:
Mol Chain Res Type Atoms2 E 1 NAG O7-C7-N2-C22 G 1 NAG O5-C5-C6-O62 E 1 NAG C8-C7-N2-C22 H 1 NAG C8-C7-N2-C22 H 1 NAG O7-C7-N2-C22 G 1 NAG C4-C5-C6-O6
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Mol Chain Res Type Atoms2 F 1 NAG O5-C5-C6-O62 G 1 NAG O7-C7-N2-C22 E 1 NAG O5-C5-C6-O62 H 1 NAG O5-C5-C6-O62 F 1 NAG C4-C5-C6-O62 G 1 NAG C8-C7-N2-C22 H 1 NAG C4-C5-C6-O62 E 1 NAG C4-C5-C6-O6
There are no ring outliers.
4 monomers are involved in 5 short contacts:
Mol Chain Res Type Clashes Symm-Clashes2 F 2 FUC 2 02 G 2 FUC 1 02 E 2 FUC 1 02 H 2 FUC 1 0
The following is a two-dimensional graphical depiction of Mogul quality analysis of bond lengths,bond angles, torsion angles, and ring geometry for oligosaccharide.
Oligosaccharide Chain E
Bond lengths Bond angles
Torsions Rings
Page 24 Full wwPDB X-ray Structure Validation Report 1FUJ
Oligosaccharide Chain F
Bond lengths Bond angles
Torsions Rings
Oligosaccharide Chain G
Bond lengths Bond angles
Torsions Rings
Page 25 Full wwPDB X-ray Structure Validation Report 1FUJ
Oligosaccharide Chain H
Bond lengths Bond angles
Torsions Rings
5.6 Ligand geometry iO
There are no ligands in this entry.
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.
Page 26 Full wwPDB X-ray Structure Validation Report 1FUJ
6 Fit of model and data iO
6.1 Protein, DNA and RNA chains iO
Unable to reproduce the depositors R factor - this section is therefore empty.
6.2 Non-standard residues in protein, DNA, RNA chains iO
Unable to reproduce the depositors R factor - this section is therefore empty.
6.3 Carbohydrates iO
Unable to reproduce the depositors R factor - this section is therefore empty.
The following is a graphical depiction of the model �t to experimental electron density for oligosac-charide. Each �t is shown from di�erent orientation to approximate a three-dimensional view.
Electron density around Chain E:
2mFo-DFc (at 0.7 rmsd) in gray
mFo-DFc (at 3 rmsd) in purple (negative)
and green (positive)
Page 27 Full wwPDB X-ray Structure Validation Report 1FUJ
Electron density around Chain F:
2mFo-DFc (at 0.7 rmsd) in gray
mFo-DFc (at 3 rmsd) in purple (negative)
and green (positive)
Electron density around Chain G:
2mFo-DFc (at 0.7 rmsd) in gray
mFo-DFc (at 3 rmsd) in purple (negative)
and green (positive)
Page 28 Full wwPDB X-ray Structure Validation Report 1FUJ
Electron density around Chain H:
2mFo-DFc (at 0.7 rmsd) in gray
mFo-DFc (at 3 rmsd) in purple (negative)
and green (positive)
6.4 Ligands iO
Unable to reproduce the depositors R factor - this section is therefore empty.
6.5 Other polymers iO
Unable to reproduce the depositors R factor - this section is therefore empty.