Download Full wwPDB X-ray Structure Validation Report i

Full wwPDB X-ray Structure Validation Report
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May 20, 2017 03:04 PM BST
PDB ID
Title
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Deposited on
Resolution
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5NXS
Crystal Structure of Human Pro-myostatin Precursor at 4.2 A Resolution with
Experimental Phases from SeMet labelling
2017-05-10
4.19 Å(reported)
This is a Full wwPDB X-ray Structure Validation Report.
This report is produced by the wwPDB biocuration pipeline after annotation of the structure.
We welcome your comments at [email protected]
A user guide is available at
http://wwpdb.org/validation/2016/XrayValidationReportHelp
with specic help available everywhere you see the i symbol.
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The following versions of software and data (see references
MolProbity
Xtriage (Phenix)
EDS
Percentile statistics
Refmac
CCP4
Ideal geometry (proteins)
Ideal geometry (DNA, RNA)
Validation Pipeline (wwPDB-VP)
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:
:
:
:
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O) were used in the production of this report:
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4.02b-467
1.9-1692
rb-20029077
20161228.v01 (using entries in the PDB archive December 28th 2016)
5.8.0135
6.5.0
Engh & Huber (2001)
Parkinson et al. (1996)
rb-20029077
Page 2
Full wwPDB X-ray Structure Validation Report
1 Overall quality at a glance
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5NXS
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The following experimental techniques were used to determine the structure:
X-RAY DIFFRACTION
The reported resolution of this entry is 4.19 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.
Metric
Rf ree
Clashscore
Ramachandran outliers
Sidechain outliers
RSRZ outliers
Whole archive
(#Entries)
100719
112137
110173
110143
101464
Similar resolution
(#Entries, resolution range(Å))
1177
1025
1024
1008
1188
(4.80-3.60)
(4.72-3.66)
(4.76-3.62)
(4.76-3.62)
(4.80-3.60)
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 indicate the
fraction of residues that contain outliers for >=3, 2, 1 and 0 types of geometric quality criteria. 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 t to the
electron density. The numeric value is given above the bar.
Mol Chain Length
1
A
335
1
B
335
Quality of chain
Page 3
Full wwPDB X-ray Structure Validation Report
2 Entry composition
5NXS
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There is only 1 type of molecule in this entry. The entry contains 3556 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 2
atoms.
ˆ Molecule 1 is a protein called Growth/differentiation factor 8.
Mol Chain Residues
1
A
290
1
B
251
Atoms
Total
C
N
O
S Se
1906 1223 311 356 11 5
Total
C
N
O S Se
1650 1055 274 307 9 5
ZeroOcc AltConf Trace
0
0
0
0
0
0
There are 4 discrepancies between the modelled and reference sequences:
Chain Residue Modelled Actual Comment
A
A
B
B
41
42
41
42
GLY
SER
GLY
SER
-
expression
expression
expression
expression
tag
tag
tag
tag
Reference
UNP
UNP
UNP
UNP
O14793
O14793
O14793
O14793
Page 4
Full wwPDB X-ray Structure Validation Report
5NXS
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3 Residue-property plots
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These plots are drawn for all protein, RNA and DNA chains in the entry. The rst graphic for
a chain summarises the proportions of the various outlier classes displayed in the second graphic.
The second graphic shows the sequence view annotated by issues in geometry and electron 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 t to the electron density (RSRZ > 2). Stretches of 2 or 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: Growth/differentiation factor 8
A330
ASN
PRO
K178
PRO
MSE
LYS
D182
T324
Q172
I173
L174
V316
F317
L318
I158
S310
Y148
Y304
K305
A306
I298
W295
F290
C281
C282
R283
S125
ASP
PHE
LEU
MSE
GLN
VAL
ASP
GLY
LYS
PRO
LYS
C137
R266
ASP
PHE
GLY
LEU
ASP
C272
A238
V239
T240
S375
P365
E232
ASN
GLY
H235
Y94
ASP
VAL
GLN
ARG
ASP
ASP
SER
SER
ASP
GLY
SER
LEU
GLU
ASP
ASP
ASP
Y111
I227
K228
N222
I359
I360
I91
M350
L87
W215
P347
K63
I56
V211
L212
T341
P342
I206
D207
V208
D195
ARG
GLY
SER
ALA
GLY
P338
I189
GLY
S42
T43
W44
Chain A:
• Molecule 1: Growth/differentiation factor 8
S375
G294
W295
D296
E291
C282
R283
P122
THR
GLU
SER
ASP
PHE
LEU
MSE
GLN
VAL
ASP
GLY
LYS
PRO
LYS
CYS
CYS
PHE
PHE
LYS
F142
D259
THR
PRO
LYS
ARG
SER
ARG
ARG
ASP
PHE
GLY
LEU
D271
P365
I118
I119
V255
I359
N354
L249
L351
A238
V239
T240
P347
I227
K228
A229
L230
Q218
P219
L194
D195
D95
VAL
GLN
ARG
ASP
ASP
SER
SER
ASP
GLY
SER
LEU
GLU
ASP
ASP
ASP
Y111
H112
A113
I72
L64
R65
L66
I56
T48
L174
R175
LEU
ILE
LYS
PRO
MSE
LYS
ASP
GLY
THR
ARG
TYR
THR
G188
I189
Y304
E314
PHE
VAL
PHE
LEU
GLN
LYS
TYR
PRO
HIS
THR
HIS
LEU
VAL
HIS
GLN
ALA
ASN
PRO
ARG
GLY
SER
ALA
GLY
PRO
C339
V171
W297
GLY
SER
THR
W44
Chain B:
Page 5
Full wwPDB X-ray Structure Validation Report
4 Data and renement statistics
Property
Space group
Cell constants
a, b, c, α, β , γ
Resolution (Å)
% Data completeness
(in resolution range)
Rmerge
Rsym
< I/σ(I) > 1
Renement 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 )
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5NXS
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Value
I23
196.83Å 196.83Å 196.83Å
90.00◦
90.00◦
90.00◦
98.41 4.19
98.42 4.19
99.7 (98.41-4.19)
100.0 (98.42-4.19)
(Not available)
(Not available)
1.61 (at 4.15Å)
BUSTER
0.274 , 0.301
0.290 , 0.308
477 reections (5.04%)
237.6
0.000
0.24 , 187.4
< |L| > = 0.45, < L2 > = 0.27
0.067 for -l,-k,-h
0.87
3556
91.0
Source
Depositor
Depositor
Depositor
EDS
Depositor
EDS
Depositor
Depositor
Xtriage
Depositor
Depositor
DCC
DCC
Xtriage
Xtriage
EDS
Xtriage
Xtriage
EDS
wwPDB-VP
wwPDB-VP
The largest o-origin peak in the Patterson
function is 2.14% of the height of the origin peak. No signicant pseudotranslation is detected.
Xtriage's analysis on translational NCS is as follows:
1 Intensities
estimated from amplitudes.
values of < |L| >, < L2 > for acentric reections are 0.5, 0.333 respectively for untwinned datasets,
and 0.375, 0.2 for perfectly twinned datasets.
2 Theoretical
Page 6
Full wwPDB X-ray Structure Validation Report
5 Model quality
5.1
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5NXS
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Standard geometry
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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 an
outlier worth inspection. RMSZ is the root-mean-square of all Z scores of the bond lengths (or
angles).
Bond lengths Bond angles
Mol Chain RMSZ
#|Z| >5 RMSZ #|Z| >5
1
1
All
A
B
All
0.50
0.48
0.49
0/1937
0/1678
0/3615
0.30
0.30
0.30
0/2668
0/2306
0/4974
There are no bond length outliers.
There are no bond angle outliers.
There are no chirality outliers.
There are no planarity outliers.
5.2
Too-close contacts
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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 hydrogen
atoms 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 Chain Non-H H(model) H(added) Clashes Symm-Clashes
1
1
All
A
B
All
1906
1650
3556
0
0
0
1570
1367
2937
17
15
29
0
0
0
The all-atom clashscore is dened as the number of clashes found per 1000 atoms (including
hydrogen atoms). The all-atom clashscore for this structure is 4.
All (29) close contacts within the same asymmetric unit are listed below, sorted by their clash
magnitude.
Atom-1
Atom-2
1:B:347:PRO:HB3
1:A:347:PRO:HB3
1:B:365:PRO:HA
1:A:365:PRO:HA
Interatomic
distance (Å)
1.66
1.67
Clash
overlap (Å)
0.77
0.76
Continued on next page...
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Full wwPDB X-ray Structure Validation Report
Continued from previous page...
Atom-1
Atom-2
1:A:359:ILE:HG23
1:A:290:PHE:HB3
1:A:318:LEU:HA
1:A:304:TYR:CE1
1:B:239:VAL:HG11
1:A:63:LYS:O
1:B:218:GLN:CB
1:B:239:VAL:O
1:A:281:CYS:HA
1:A:360:ILE:HG12
1:A:208:VAL:HG22
1:B:351:LEU:HD11
1:A:158:ILE:HD12
1:B:271:ASP:HA
1:A:215:TRP:CD1
1:B:227:ILE:HD12
1:A:227:ILE:HD12
1:B:64:LEU:HB3
1:A:173:ILE:HG22
1:B:171:VAL:HA
1:B:118:ILE:HG13
1:B:72:ILE:HD11
1:A:341:THR:OG1
1:B:295:TRP:HB2
1:A:174:LEU:HD21
1:A:298:ILE:HG21
1:A:172:GLN:HE21
1:B:119:ILE:HB
1:A:295:TRP:HB2
1:A:324:THR:HG23
1:A:306:ALA:HB2
1:B:249:LEU:O
1:B:113:ALA:HB2
1:B:219:PRO:HD3
1:B:239:VAL:HG13
1:A:310:SER:O
1:B:118:ILE:HG22
1:A:211:VAL:HB
1:B:359:ILE:HG22
1:A:206:ILE:HD13
1:B:283:ARG:O
1:A:222:ASN:HA
1:B:238:ALA:HB1
1:A:238:ALA:HB1
1:B:66:LEU:HD12
1:A:189:ILE:HD12
1:B:228:LYS:O
1:B:255:VAL:HG13
1:B:297:TRP:HB3
1:A:342:PRO:HD2
1:B:297:TRP:CD1
1:A:228:LYS:HE3
1:A:350:MSE:HE2
1:A:228:LYS:HD2
Interatomic
distance (Å)
1.68
1.78
1.82
2.39
2.04
2.06
2.37
2.07
2.06
1.92
1.93
1.94
1.93
2.13
2.48
1.97
1.98
1.99
2.00
2.18
2.01
2.01
2.20
2.56
2.02
2.02
1.85
5NXS
Clash
overlap (Å)
0.74
0.65
0.60
0.57
0.57
0.56
0.55
0.55
0.55
0.51
0.51
0.50
0.50
0.49
0.49
0.47
0.45
0.44
0.44
0.43
0.42
0.41
0.41
0.41
0.41
0.40
0.40
There are no symmetry-related clashes.
5.3
Torsion angles
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5.3.1 Protein backbone O
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In the following table, the Percentiles column shows the percent Ramachandran outliers of the
chain 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 was
analysed, and the total number of residues.
Page 8
Full wwPDB X-ray Structure Validation Report
Mol Chain
Analysed
1
A
276/335 (82%)
1
B
All
All
5NXS
Favoured Allowed Outliers Percentiles
246 (89%)
28 (10%)
2 (1%)
25
68
239/335 (71%)
206 (86%)
30 (13%)
3 (1%)
14
56
515/670 (77%)
452 (88%)
58 (11%)
5 (1%)
18
61
All (5) Ramachandran outliers are listed below:
Mol Chain Res Type
1
1
1
1
1
A
B
B
A
B
281
218
294
283
189
CYS
GLN
GLY
ARG
ILE
5.3.2 Protein sidechains O
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In the following table, the Percentiles column shows the percent sidechain outliers of the chain 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 sidechain conformation was
analysed, and the total number of residues.
Mol Chain
Analysed
1
A
154/295 (52%)
1
B
All
All
Rotameric Outliers Percentiles
140 (91%)
14 (9%)
11
42
135/295 (46%)
122 (90%)
13 (10%)
10
39
289/590 (49%)
262 (91%)
27 (9%)
10
41
All (27) residues with a non-rotameric sidechain are listed below:
Mol Chain Res Type
1
1
1
1
1
1
1
1
1
1
1
A
A
A
A
A
A
A
A
A
A
A
44
56
87
91
137
148
174
195
212
240
272
TRP
ILE
LEU
ILE
CYS
TYR
LEU
ASP
LEU
THR
CYS
Continued on next page...
Page 9
Full wwPDB X-ray Structure Validation Report
5NXS
Continued from previous page...
Mol Chain Res Type
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
A
A
A
B
B
B
B
B
B
B
B
B
B
B
B
B
282
304
316
48
56
72
112
174
194
195
230
240
282
291
304
354
CYS
TYR
VAL
THR
ILE
ILE
HIS
LEU
LEU
ASP
LEU
THR
CYS
GLU
TYR
ASN
Some sidechains can be ipped to improve hydrogen bonding and reduce clashes. All (3) such
sidechains are listed below:
Mol Chain Res Type
1
1
1
A
A
B
93
172
172
GLN
GLN
GLN
5.3.3 RNA O
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There are no RNA molecules in this entry.
5.4
Non-standard residues in protein, DNA, RNA chains
There are no non-standard protein/DNA/RNA residues in this entry.
5.5
Carbohydrates
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There are no carbohydrates in this entry.
5.6
Ligand geometry
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There are no ligands in this entry.
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Page 10
5.7
Full wwPDB X-ray Structure Validation Report
Other polymers
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There are no such residues in this entry.
5.8
Polymer linkage issues
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There are no chain breaks in this entry.
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5NXS
Page 11
Full wwPDB X-ray Structure Validation Report
6 Fit of model and data
6.1
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Protein, DNA and RNA chains
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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 to
all 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 per
residue. The column labelled `Q< 0.9' lists the number of (and percentage) of residues with an
average occupancy less than 0.9.
Mol Chain
Analysed
RSRZ>
<
1
A
285/335 (85%)
1
B
All
All
RSRZ>2
#
OWAB(Å ) Q<0.9
2
-0.43
0 100
100
10, 94, 150, 243
0
246/335 (73%)
-0.50
0 100
100
25, 94, 132, 267
0
531/670 (79%)
-0.46
0 100
100
10, 94, 143, 267
0
There are no RSRZ outliers to report.
6.2
Non-standard residues in protein, DNA, RNA chains
There are no non-standard protein/DNA/RNA residues in this entry.
6.3
Carbohydrates
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There are no carbohydrates in this entry.
6.4
Ligands
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There are no ligands in this entry.
6.5
Other polymers
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There are no such residues in this entry.
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