wwPDB X-ray Structure Validation Summary Report
O
i
Jan 5, 2015 – 08:03 PM EST
PDB ID : 4REB
Title : Structural Insights into 5’ Flap DNA Unwinding and Incision by the Human
FAN1 Dimer
Authors : Zhao, Q.; Xue, X.; Longerich, S.; Sung, P.; Xiong, Y.
Deposited on : 2014-09-22
Resolution : 4.20 ˚
A(reported)
This is a wwPDB validation summary report for a publicly released PDB entry.
We welcome your comments at [email protected]
A user guide is available at http://wwpdb.org/ValidationPDFNotes.html
The following versions of software and data (see references) were used in the production of this report:
MolProbity
Mogul
Xtriage (Phenix)
EDS
Percentile statistics
Refmac
CCP4
Ideal geometry (proteins)
Ideal geometry (DNA, RNA)
Validation Pipeline (wwPDB-VP)
:
:
:
:
:
:
:
:
:
:
4.02b-467
1.16 November 2013
dev-1439
stable24195
21963
5.8.0049
6.1.3
Engh & Huber (2001)
Parkinson et. al. (1996)
stable24195
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wwPDB X-ray Structure Validation Summary Report
Overall quality at a glance
O
4REB
i
The reported resolution of this entry is 4.20 ˚
A.
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)
66092
79885
78287
78261
66119
Similar resolution
(#Entries, resolution range(˚
A))
1001 (4.84-3.50)
1259 (4.84-3.50)
1192 (4.84-3.50)
1175 (4.84-3.50)
1001 (4.84-3.50)
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 on the lower bar indicate the
fraction of residues that contain outliers for >=3, 2, 1 and 0 types of geometric quality criteria.
The upper red bar (where present) indicates the fraction of residues that have poor fit to the
electron density.
Mol
1
2
3
4
4
Chain
D
E
F
A
H
Length
9
20
10
647
647
Quality of chain
The following table lists non-polymeric compounds that are outliers for geometric or electrondensity-fit criteria:
Mol
5
5
Type
SM
SM
Chain
A
H
Res
1101
1101
Geometry
-
Electron density
X
X
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wwPDB X-ray Structure Validation Summary Report
Entry composition
4REB
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There are 5 unique types of molecules in this entry. The entry contains 10114 atoms, of which 0
are hydrogen and 0 are deuterium.
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 DNA chain called DNA (5’-D(P*GP*TP*GP*GP*CP*GP*AP*GP*C)-3’).
Mol
Chain
Residues
1
D
9
Atoms
Total C N O
189 88 38 54
ZeroOcc
AltConf
Trace
0
0
0
P
9
ˆ Molecule 2 is a DNA chain called DNA (5’-D(P*CP*GP*TP*GP*GP*CP*GP*AP*GP*CP
*GP*CP*TP*CP*GP*CP*CP*AP*CP*G)-3’).
Mol
Chain
Residues
2
E
20
Atoms
Total C
N O
410 192 78 120
ZeroOcc
AltConf
Trace
0
0
0
P
20
ˆ Molecule 3 is a DNA chain called DNA (5’-D(P*GP*CP*TP*CP*GP*CP*CP*AP*CP*G)3’).
Mol
Chain
Residues
3
F
10
Atoms
Total C N O
202 95 37 60
ZeroOcc
AltConf
Trace
0
0
0
P
10
ˆ Molecule 4 is a protein called Fanconi-associated nuclease 1.
Mol
Chain
Residues
4
A
566
4
H
584
Total
4590
Total
4721
Atoms
C
N
2931 815
C
N
3014 841
O
821
O
843
S
23
S
23
ZeroOcc
AltConf
Trace
0
1
0
0
1
0
There are 6 discrepancies between the modelled and reference sequences:
Chain
A
A
A
H
Residue
371
372
960
371
Modelled
GLU
PHE
ALA
GLU
Actual
ASP
-
Comment
Reference
EXPRESSION TAG
UNP Q9Y2M0
EXPRESSION TAG
UNP Q9Y2M0
ENGINEERED MUTATION UNP Q9Y2M0
EXPRESSION TAG
UNP Q9Y2M0
Continued on next page...
Page 4
wwPDB X-ray Structure Validation Summary Report
Continued from previous page...
Chain Residue Modelled Actual
H
372
PHE
H
960
ALA
ASP
Comment
EXPRESSION TAG
ENGINEERED MUTATION
4REB
Reference
UNP Q9Y2M0
UNP Q9Y2M0
ˆ Molecule 5 is SAMARIUM (III) ION (three-letter code: SM) (formula: Sm).
Mol
Chain
Residues
5
H
1
5
A
1
Atoms
Total Sm
1
1
Total Sm
1
1
ZeroOcc
AltConf
0
0
0
0
Page 5
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wwPDB X-ray Structure Validation Summary Report
Residue-property plots
4REB
O
i
These plots are drawn for all protein, RNA and DNA chains in the entry. The first graphic for a
chain summarises the proportions of errors displayed in the second graphic. The second graphic
shows the sequence view annotated by issues in geometry and electron density. Residues are colorcoded 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 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: DNA (5’-D(P*GP*TP*GP*GP*CP*GP*AP*GP*C)-3’)
G5
C6
G7
A8
G9
C10
G2
Chain D:
• Molecule 2: DNA (5’-D(P*CP*GP*TP*GP*GP*CP*GP*AP*GP*CP*GP*CP*TP*CP*GP*C
P*CP*AP*CP*G)-3’)
A8
G9
C10
G11
C12
T13
C14
G15
C16
C17
A18
C19
G20
C1
Chain E:
• Molecule 3: DNA (5’-D(P*GP*CP*TP*CP*GP*CP*CP*AP*CP*G)-3’)
C31
G32
G23
C24
T25
C26
G27
Chain F:
• Molecule 4: Fanconi-associated nuclease 1
•
F455
L456
Q457
T458
E459
E448
E449
L450
P445
Y436
E437
K433
•
K425
L426
S427
W428
I429
K430
L410
S411
A412
T413
G414
Q415
K416
L417
Y418
V419
R420
I403
Q399
E400
V386
E390
D391
D392
M393
K539
A531
G532
Q533
S534
V535
R536
R636
D637
W638
N639
R640
L641
K642
N643
L719
K720
R721
L722
E723
P724
T725
I726
L630
A631
Q632
C633
H716
L713
L602
D709
R710
R591
K592
T593
R704
G705
Y699
C700
P701
L694
S695
Q696
Y683
E684
E685
A686
V687
I676
L677
Q678
R679
F673
P585
•
L503
A504
LYS
GLN
ARG
SER
VAL
CYS
THR
TRP
GLY
LYS
ASN
LYS
PRO
GLY
ILE
GLY
ALA
VAL
ILE
LEU
LYS
R526
Q492
K493
Q494
Q495
K482
T483
F484
H485
L486
L670
T667
T781
I782
T783
GLY
ARG
LEU
CYS
PRO
GLN
ARG
GLY
MET
CYS
LYS
SER
VAL
PHE
VAL
MET
GLU
ALA
GLY
M772
ALA
VAL
GLN
ASP
V777
L769
C759
K760
K761
F762
K763
H764
L765
F766
•
W664
V751
R752
L753
R754
E755
L551
T555
ASP
SER
MET
GLU
ASP
GLU
ASP
ALA
ALA
CYS
GLY
GLY
GLN
GLY
GLN
LEU
SER
THR
VAL
L575
L576
V577
N578
L579
G580
R581
M582
R658
C659
F660
T661
R547
V738
R739
T740
G741
H742
R743
L744
S745
L746
Y747
Q748
L733
•
•
•
H644
P645
S646
L647
R648
C649
H650
E651
G540
P541
R542
A543
V544
•
V468
L469
E470
L471
L472
S473
A474
P475
E476
L477
K478
•
Y374
Y375
L376
R377
S378
F379
L380
V381
V382
L465
•
•
E371
L462
•
Chain A:
H1005
V1006
V1007
A1008
VAL
GLY
ALA
LYS
SER
GLN
SER
LEU
SER
E1000
V1001
E1002
Q995
M988
I989
W990
L991
A992
R982
L983
S984
H985
K977
S968
R969
H970
F971
K972
L973
V974
L958
P959
A960
L961
V962
D950
F951
R952
H953
C954
R955
L947
•
•
•
I831
V943
C944
L889
R886
R880
T872
D873
S874
F875
F876
T877
D869
F866
L844
L845
L846
W847
L841
T837
F838
R823
•
•
GLY
MET
CYS
LYS
SER
VAL
PHE
VAL
MET
GLU
ALA
GLY
GLU
ALA
ALA
ASP
PRO
THR
THR
VAL
LEU
C812
S813
V814
E815
E816
L817
A818
L819
L940
L935
G936
A928
Q929
F922
A914
S915
L916
V917
S918
T905
W906
H907
E908
Q909
E910
S897
L898
R899
A900
W901
V902
I890
•
•
•
•
•
•
•
•
R785
LEU
CYS
PRO
GLN
ARG
I782
D776
V777
L769
P770
L765
F766
L753
R754
E755
S756
P757
S758
C759
K760
K761
F762
L744
S745
L746
Y747
Q748
R749
G732
L733
I729
N714
L715
H716
Q717
H718
L719
K720
R721
L722
E723
P724
T725
I726
W707
W708
D709
R710
L711
•
•
•
•
•
•
•
•
•
•
•
R704
G705
R706
L694
S695
Q696
R697
I698
Y699
Y683
E684
E685
A686
V687
R688
E689
L690
F673
V674
E675
I676
L677
Q678
R679
I669
L670
W664
I665
Y666
H650
E651
D652
L653
P654
L655
F656
L657
R658
C659
R636
D637
W638
N639
R640
L641
K642
N643
L630
A631
Q632
N621
•
•
•
•
•
I615
S616
S617
A618
M619
A620
R599
F596
T593
T588
I548
L549
L550
L551
F552
S553
L554
T555
ASP
SER
MET
GLU
ASP
GLU
ASP
ALA
ALA
CYS
GLY
GLY
GLN
GLY
GLN
LEU
SER
THR
VAL
L575
L576
V577
N578
L579
R542
A543
V544
K539
S534
A527
K528
A529
L530
I519
G520
A521
V522
I523
L524
K525
R526
K505
Q506
ARG
SER
VAL
CYS
THR
TRP
GLY
LYS
ASN
K516
L501
V487
N488
P489
N490
G491
Q492
K493
Q494
Q495
K482
T483
F484
V468
L469
E470
L471
L472
S473
A474
P475
E476
L477
L465
L462
E459
F455
L456
E449
L450
•
•
L443
Y436
E437
E438
I439
A440
Q415
K416
L417
Y418
V419
R420
L421
F422
Q423
R424
K425
L426
S427
W428
K406
F407
Y408
Q409
L410
S411
A412
I403
Q399
E400
M393
L394
L395
F396
E371
F372
P373
Y374
Y375
L376
R377
S378
F379
L380
V381
V382
L383
K384
T385
V386
L387
E388
•
•
H1005
V1006
V1007
A1008
VAL
GLY
ALA
LYS
SER
GLN
SER
LEU
SER
E1002
L994
W990
•
R982
L983
K972
L973
V974
E975
V976
K977
G978
P979
L958
P959
A960
L961
V962
V963
D950
F951
R952
H953
C954
C944
R945
H946
L947
L940
V932
Q929
L925
W919
D920
R921
L916
R912
V902
A903
A904
T905
W906
H907
E908
Q909
E896
S897
L898
R899
•
•
•
•
•
•
•
•
•
•
•
•
A893
R886
L887
Q888
L889
F866
P867
L868
D869
L870
C871
T872
D873
S874
F875
F876
T877
D848
L841
Y842
G843
L844
L845
F838
E834
Y822
R823
R824
S825
G826
F827
D828
Q829
G830
GLU
ALA
ALA
ASP
PRO
THR
THR
VAL
LEU
C812
S813
V814
E815
E816
L817
A818
L819
•
•
•
•
•
•
•
•
Page 6
wwPDB X-ray Structure Validation Summary Report
4REB
• Molecule 4: Fanconi-associated nuclease 1
Chain H:
Page 7
4
wwPDB X-ray Structure Validation Summary Report
Data and refinement statistics
Property
Space group
Cell constants
a, b, c, α, β, γ
Resolution (˚
A)
% Data completeness
(in resolution range)
Rmerge
Rsym
< I/σ(I) > 1
Refinement program
R, Rf ree
Rf ree test set
Wilson B-factor (˚
A2 )
Anisotropy
Bulk solvent ksol (e/˚
A3 ), Bsol (˚
A2 )
Estimated twinning fraction
Reported twinning fraction
L-test for twinning
Outliers
Fo ,Fc correlation
Total number of atoms
Average B, all atoms (˚
A2 )
O
4REB
i
Value
P 31
˚
104.77A 104.77˚
A 127.55˚
A
◦
◦
90.00
90.00
120.00◦
90.70 – 4.20
90.73 – 4.20
99.3 (90.70-4.20)
99.3 (90.73-4.20)
0.08
(Not available)
1.53 (at 4.15˚
A)
REFMAC 5.7.0029
0.230 , 0.262
0.234 , 0.266
566 reflections (5.24%)
247.1
0.085
0.29 , 241.9
0.495 for H, K, L
0.505 for K, H, -L
0.196 for -h,-k,l
0.359 for h,-h-k,-l
0.198 for -k,-h,-l
0.495 for H, K, L
0.505 for K, H, -L
< |L| > = 0.36, < L2 > = 0.19
0 of 11360 reflections
0.96
10114
297.0
Source
Depositor
Depositor
Depositor
EDS
Depositor
EDS
Depositor
Depositor
Xtriage
Depositor
Depositor
DCC
DCC
Xtriage
Xtriage
EDS
Xtriage
Depositor
Xtriage
Xtriage
EDS
wwPDB-VP
wwPDB-VP
Xtriage’s analysis on translational NCS is as follows: The largest off-origin peak in the Patterson
function is 3.46% of the height of the origin peak. No significant pseudotranslation is detected.
1
Intensities estimated from amplitudes.
Page 8
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wwPDB X-ray Structure Validation Summary Report
O
Model quality
5.1
4REB
i
Standard geometry
O
i
Bond lengths and bond angles in the following residue types are not validated in this section:
SM
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).
Mol
Chain
1
2
3
4
4
All
D
E
F
A
H
All
Bond lengths
RMSZ #|Z| >5
0.49
0/212
0.44
0/459
0.48
0/225
0.57
0/4689
0.57
0/4822
0.56
0/10407
Bond angles
RMSZ
#|Z| >5
0.84
1/326 (0.3%)
0.75
0/706
0.75
0/344
0.79
6/6339 (0.1%)
0.80
3/6518 (0.0%)
0.79
10/14233 (0.1%)
There are no bond length outliers.
The worst 5 of 10 bond angle outliers are listed below:
Mol
4
4
4
4
4
Chain
H
A
H
A
H
Res
421
471
889
630
387
Type
LEU
LEU
LEU
LEU
LEU
Atoms
CB-CG-CD2
CA-CB-CG
CA-CB-CG
CB-CG-CD2
CA-CB-CG
Z
-6.66
6.04
5.80
5.79
5.79
Observed(o )
99.68
129.18
128.63
120.85
128.61
Ideal(o )
111.00
115.30
115.30
111.00
115.30
There are no chirality outliers.
There are no planarity outliers.
5.2
Close contacts
O
i
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 hydrogens
added by MolProbity. The Clashes column lists the number of clashes within the asymmetric unit,
and the number in parentheses is this value normalized per 1000 atoms of the molecule in the
chain. The Symm-Clashes column gives symmetry related clashes, in the same way as for the
Clashes column.
Page 9
Mol
1
2
3
4
4
5
5
All
wwPDB X-ray Structure Validation Summary Report
Chain
D
E
F
A
H
A
H
All
Non-H
189
410
202
4590
4721
1
1
10114
H(model)
0
0
0
0
0
0
0
0
H(added)
101
223
112
4602
4752
0
0
9790
Clashes
6
13
3
205
214
0
0
431
4REB
Symm-Clashes
0
1
0
1
2
0
0
2
Clashscore is defined as the number of clashes calculated for the entry per 1000 atoms (including
hydrogens) of the entry. The overall clashscore for this entry is 22.
The worst 5 of 431 close contacts within the same asymmetric unit are listed below.
Atom-1
4:A:579:LEU:HB2
4:A:579:LEU:HA
4:H:374:TYR:CE2
4:A:579:LEU:CA
4:A:579:LEU:CB
Atom-2
4:A:582:MET:CE
4:A:582:MET:CG
4:H:577:VAL:HG13
4:A:582:MET:HG2
4:A:582:MET:CE
Distance(˚
A)
1.39
1.43
1.52
1.50
2.12
Clash(˚
A)
1.47
1.47
1.42
1.36
1.26
All (2) symmetry-related close contacts are listed below. The label for Atom-2 includes the symmetry operator and encoded unit-cell translations to be applied.
Atom-1
4:A:580:GLY:O
2:E:19:DC:OP2
5.3
5.3.1
Atom-2
4:H:688:ARG:NH2[3 664]
4:H:436:TYR:OH[2 545]
Torsion angles
Distance(˚
A)
1.97
2.07
Clash(˚
A)
0.23
0.13
O
Protein backbone i
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.
Mol
Chain
Analysed
Favoured
Allowed
Outliers
4
A
557/647 (86%)
539 (97%)
17 (3%)
1 (0%)
4
H
577/647 (89%)
552 (96%)
22 (4%)
Percentiles
56
93
3 (0%)
38 88
Continued on next page...
Page 10
wwPDB X-ray Structure Validation Summary Report
Continued from previous page...
Mol Chain
Analysed
All
All
1134/1294 (88%)
Favoured
Allowed
Outliers
1091 (96%)
39 (3%)
4 (0%)
4REB
Percentiles
43
90
All (4) Ramachandran outliers are listed below:
Mol
4
4
4
4
5.3.2
Chain
A
H
H
H
Res
642
490
757
777
Type
LYS
ASN
PRO
VAL
O
Protein sidechains i
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
Rotameric
Outliers
Percentiles
4
A
498/562 (89%)
459 (92%)
39 (8%)
18
64
4
H
511/562 (91%)
473 (93%)
38 (7%)
20
66
All
All
1009/1124 (90%)
932 (92%)
77 (8%)
19
65
5 of 77 residues with a non-rotameric sidechain are listed below:
Mol
4
4
4
4
4
Chain
A
H
H
A
H
Res
872
522
935
907
387
Type
THR
VAL
LEU
HIS
LEU
Some sidechains can be flipped to improve hydrogen bonding and reduce clashes. All (5) such
sidechains are listed below:
Mol
4
4
4
4
4
Chain
A
A
H
H
H
Res
678
714
678
714
718
Type
GLN
ASN
GLN
ASN
HIS
Page 11
5.3.3
wwPDB X-ray Structure Validation Summary Report
4REB
O
RNA i
There are no RNA chains in this entry.
5.4
Non-standard residues in protein, DNA, RNA chains
O
i
There are no non-standard protein/DNA/RNA residues in this entry.
5.5
Carbohydrates
O
i
There are no carbohydrates in this entry.
5.6
Ligand geometry
O
i
Of 2 ligands modelled in this entry, 2 are monoatomic - leaving 0 for Mogul analysis.
There are no bond length outliers.
There are no bond angle outliers.
There are no chirality outliers.
There are no torsion outliers.
There are no ring outliers.
5.7
Other polymers
O
i
There are no such residues in this entry.
5.8
Polymer linkage issues
There are no chain breaks in this entry.
Page 12
6
wwPDB X-ray Structure Validation Summary Report
Fit of model and data
6.1
O
4REB
i
Protein, DNA and RNA chains
O
i
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.
˚2 )
OWAB(A
Q<0.9
100
292, 298, 305, 312
0
0 100
100
268, 286, 307, 312
0
-0.12
0 100
100
248, 263, 328, 352
0
566/647 (87%)
0.34
33 (5%) 22
22
243, 294, 353, 396
0
H
584/647 (90%)
0.32
33 (5%) 23
22
218, 299, 364, 449
0
All
1189/1333 (89%)
0.31
66 (5%) 24
22
218, 295, 358, 449
0
Mol
Chain
Analysed
<RSRZ>
#RSRZ>2
1
D
9/9 (100%)
-0.48
0 100
2
E
20/20 (100%)
-0.21
3
F
10/10 (100%)
4
A
4
All
The worst 5 of 66 RSRZ outliers are listed below:
Mol
4
4
4
4
4
6.2
Chain
H
H
H
H
A
Res
753
697
845
685
1002
Type
LEU
ARG
LEU
GLU
GLU
RSRZ
5.4
4.4
4.3
3.9
3.9
Non-standard residues in protein, DNA, RNA chains
O
i
There are no non-standard protein/DNA/RNA residues in this entry.
6.3
Carbohydrates
O
i
There are no carbohydrates in this entry.
6.4
Ligands
O
i
In the following table, the Atoms column lists the number of modelled atoms in the group and the
number defined in the chemical component dictionary. LLDF column lists the quality of electron
Page 13
wwPDB X-ray Structure Validation Summary Report
4REB
density of the group with respect to its neighbouring residues in protein, DNA or RNA chains.
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
5
5
6.5
Type
SM
SM
Chain
A
H
Res
1101
1101
Other polymers
Atoms
1/1
1/1
O
i
There are no such residues in this entry.
RSR
0.30
0.25
LLDF
5.60
2.74
B-factors(˚
A2 )
340,340,340,340
386,386,386,386
Q<0.9
0
0

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