14
Full wwPDB X-ray Structure Validation Report iO
May 22, 2020 � 04:04 am BST
PDB ID : 3FCITitle : Complex of UNG2 and a fragment-based designed inhibitor
Authors : Bianchet, M.A.; Chung, S.; Parker, J.B.; Amzel, L.M.; Stivers, J.T.Deposited on : 2008-11-21Resolution : 1.27 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 : 2.11
buster-report : 1.1.7 (2018)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) : 2.11
Page 2 Full wwPDB X-ray Structure Validation Report 3FCI
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 1.27 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))
Rfree 130704 1850 (1.30-1.26)Clashscore 141614 1926 (1.30-1.26)
Ramachandran outliers 138981 1860 (1.30-1.26)Sidechain outliers 138945 1859 (1.30-1.26)RSRZ outliers 127900 1807 (1.30-1.26)
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% The upper red bar (where present) indicates the fraction of residuesthat have poor �t to the electron density. The numeric value is given above the bar.
Mol Chain Length Quality of chain
1 A 223
The following table lists non-polymeric compounds, carbohydrate monomers and non-standardresidues in protein, DNA, RNA chains that are outliers for geometric or electron-density-�t crite-ria:
Mol Type Chain Res Chirality Geometry Clashes Electron density2 3FI A 1 - X - -
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2 Entry composition iO
There are 5 unique types of molecules in this entry. The entry contains 2356 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 Uracil-DNA glycosylase.
Mol Chain Residues Atoms ZeroOcc AltConf Trace
1 A 223Total C N O S1829 1182 321 320 6
0 2 0
There are 3 discrepancies between the modelled and reference sequences:
Chain Residue Modelled Actual Comment ReferenceA 82 MET - INSERTION UNP P13051A 83 GLU - INSERTION UNP P13051A 84 PHE - INSERTION UNP P13051
� Molecule 2 is 3-{(E)-[(3-{[(2,6-dioxo-1,2,3,6-tetrahydropyrimidin-4-yl)methyl]amino}propoxy)imino]methyl}benzoic acid (three-letter code: 3FI) (formula: C16H18N4O5).
Mol Chain Residues Atoms ZeroOcc AltConf
2 A 1Total C N O25 16 4 5
0 0
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� Molecule 3 is SODIUM ION (three-letter code: NA) (formula: Na).
Mol Chain Residues Atoms ZeroOcc AltConf
3 A 1Total Na1 1
0 0
� Molecule 4 is THIOCYANATE ION (three-letter code: SCN) (formula: CNS).
Mol Chain Residues Atoms ZeroOcc AltConf
4 A 1Total C N S3 1 1 1
0 0
4 A 1Total C N S3 1 1 1
0 0
� Molecule 5 is water.
Mol Chain Residues Atoms ZeroOcc AltConf
5 A 495Total O495 495
0 0
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3 Residue-property plots iO
These plots are drawn for all protein, RNA and DNA chains in the entry. The �rst graphic fora 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 theycontain at least one outlier: green = 0, yellow = 1, orange = 2 and red = 3 or more. A red dotabove a residue indicates a poor �t to the electron density (RSRZ > 2). 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: Uracil-DNA glycosylase
Chain A:
M82
E83•
F84
F85
K90
I103
K104
Y116•
K135
I181
E182•
D183•
F184
V185•
H189
G190
D191
R210
W232
Q235
W245
Y248•
A249
Q250
Q265
S270
R276•
H283
K302
E303
L304
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4 Data and re�nement statistics iO
Property Value SourceSpace group P 21 21 21 DepositorCell constantsa, b, c, α, β, γ
43.01Å 68.48Å 69.67Å90.00◦ 90.00◦ 90.00◦
Depositor
Resolution (Å)27.08 � 1.2727.07 � 1.27
DepositorEDS
% Data completeness(in resolution range)
80.9 (27.08-1.27)80.9 (27.07-1.27)
DepositorEDS
Rmerge 0.06 DepositorRsym (Not available) Depositor
< I/σ(I) > 1 2.30 (at 1.27Å) XtriageRe�nement program REFMAC 5.2.0019 Depositor
R, Rfree0.174 , 0.2070.171 , 0.205
DepositorDCC
Rfree test set 2283 re�ections (5.07%) wwPDB-VPWilson B-factor (Å2) 14.9 Xtriage
Anisotropy 0.179 XtriageBulk solvent ksol(e/Å3), Bsol(Å2) 0.32 , 41.9 EDS
L-test for twinning2 < |L| > = 0.49, < L2 > = 0.32 XtriageEstimated twinning fraction 0.016 for -h,l,k Xtriage
Fo,Fc correlation 0.97 EDSTotal number of atoms 2356 wwPDB-VP
Average B, all atoms (Å2) 18.0 wwPDB-VP
Xtriage's analysis on translational NCS is as follows: The largest o�-origin peak in the Patterson
function is 8.29% 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.
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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: NA,SCN, 3FI
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 anglesRMSZ #|Z| >5 RMSZ #|Z| >5
1 A 0.46 0/1891 0.59 0/2563
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 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 1829 0 1777 19 02 A 25 0 17 0 03 A 1 0 0 0 04 A 6 0 0 0 05 A 495 0 0 10 0All All 2356 0 1794 19 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 5.
All (19) close contacts within the same asymmetric unit are listed below, sorted by their clashmagnitude.
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Atom-1 Atom-2Interatomicdistance (Å)
Clashoverlap (Å)
1:A:248[B]:TYR:CZ 5:A:65:HOH:O 1.79 1.321:A:189:HIS:HD2 1:A:191:ASP:H 1.21 0.881:A:181:ILE:HG21 5:A:558:HOH:O 1.75 0.861:A:235:GLN:HB2 5:A:481:HOH:O 1.77 0.841:A:245:TRP:HE1 1:A:283:HIS:HD2 1.28 0.811:A:232:TRP:HA 5:A:481:HOH:O 1.86 0.751:A:245:TRP:HE1 1:A:283:HIS:CD2 2.13 0.661:A:116:TYR:CD1 1:A:210:ARG:HD3 2.31 0.661:A:303:GLU:HG3 5:A:647:HOH:O 1.96 0.661:A:85:PHE:HB3 1:A:90:LYS:HZ3 1.67 0.591:A:135:LYS:HE3 5:A:485:HOH:O 2.02 0.571:A:250:GLN:HG2 1:A:265:GLN:HE21 1.72 0.551:A:302:LYS:HG3 5:A:558:HOH:O 2.06 0.541:A:189:HIS:CD2 1:A:191:ASP:H 2.13 0.501:A:104:LYS:HE2 5:A:36:HOH:O 2.13 0.471:A:85:PHE:HB3 1:A:90:LYS:NZ 2.29 0.461:A:103:ILE:HD12 5:A:519:HOH:O 2.15 0.451:A:283:HIS:HE1 5:A:534:HOH:O 1.98 0.451:A:183:ASP:HB2 1:A:302:LYS:HD3 1.99 0.44
There are no symmetry-related clashes.
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 223/223 (100%) 217 (97%) 6 (3%) 0 100 100
There are no Ramachandran outliers to report.
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 similar
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resolution.
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 197/195 (101%) 194 (98%) 3 (2%) 65 30
All (3) residues with a non-rotameric sidechain are listed below:
Mol Chain Res Type1 A 183 ASP1 A 270 SER1 A 283 HIS
Some sidechains can be �ipped to improve hydrogen bonding and reduce clashes. All (3) suchsidechains are listed below:
Mol Chain Res Type1 A 124 GLN1 A 189 HIS1 A 283 HIS
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
There are no carbohydrates in this entry.
5.6 Ligand geometry iO
Of 4 ligands modelled in this entry, 1 is monoatomic - leaving 3 for Mogul analysis.
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 bond
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length (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
4 SCN A 3 - 1,2,2 1.40 0 0,1,1 0.00 -2 3FI A 1 - 22,26,26 1.69 8 (36%) 23,33,33 4.08 15 (65%)4 SCN A 2 - 1,2,2 0.30 0 0,1,1 0.00 -
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.
Mol Type Chain Res Link Chirals Torsions Rings2 3FI A 1 - - 8/11/15/15 0/2/2/2
All (8) bond length outliers are listed below:
Mol Chain Res Type Atoms Z Observed(Å) Ideal(Å)2 A 1 3FI C5-C38 3.74 1.51 1.472 A 1 3FI C16-N11 3.05 1.39 1.342 A 1 3FI C9-N18 2.84 1.33 1.272 A 1 3FI O33-C14 2.80 1.31 1.242 A 1 3FI C4-C5 2.28 1.43 1.392 A 1 3FI O1-C22 -2.16 1.40 1.432 A 1 3FI C30-C16 2.08 1.55 1.512 A 1 3FI C3-C9 2.03 1.51 1.47
All (15) bond angle outliers are listed below:
Mol Chain Res Type Atoms Z Observed(o) Ideal(o)2 A 1 3FI O1-N18-C9 9.69 125.69 110.802 A 1 3FI C3-C9-N18 7.99 144.68 120.502 A 1 3FI C30-C16-C15 -7.00 107.92 120.512 A 1 3FI C30-C16-N11 5.98 127.12 116.612 A 1 3FI C3-C4-C5 -4.96 115.28 121.082 A 1 3FI C6-C5-C38 -4.52 114.30 120.372 A 1 3FI C2-C3-C9 -4.23 111.80 120.812 A 1 3FI C15-C14-N13 4.03 128.79 124.082 A 1 3FI C2-C3-C4 3.53 123.11 118.712 A 1 3FI C6-C5-C4 2.74 122.04 118.162 A 1 3FI C30-N31-C8 2.73 122.77 113.41
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Page 11 Full wwPDB X-ray Structure Validation Report 3FCI
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Mol Chain Res Type Atoms Z Observed(o) Ideal(o)2 A 1 3FI C4-C5-C38 2.51 123.67 120.362 A 1 3FI C4-C3-C9 2.46 125.08 120.432 A 1 3FI C22-O1-N18 2.30 111.63 109.212 A 1 3FI C14-C15-C16 -2.26 110.63 117.22
There are no chirality outliers.
All (8) torsion outliers are listed below:
Mol Chain Res Type Atoms2 A 1 3FI C9-N18-O1-C222 A 1 3FI C23-C22-O1-N182 A 1 3FI O1-C22-C23-C82 A 1 3FI C22-C23-C8-N312 A 1 3FI C2-C3-C9-N182 A 1 3FI C4-C3-C9-N182 A 1 3FI N11-C16-C30-N312 A 1 3FI C15-C16-C30-N31
There are no ring outliers.
No monomer is involved in short contacts.
The following is a two-dimensional graphical depiction of Mogul quality analysis of bond lengths,bond angles, torsion angles, and ring geometry for all instances of the Ligand of Interest. Inaddition, ligands with molecular weight > 250 and outliers as shown on the validation Tables willalso be included. For torsion angles, if less then 5% of the Mogul distribution of torsion angles iswithin 10 degrees of the torsion angle in question, then that torsion angle is considered an outlier.Any bond that is central to one or more torsion angles identi�ed as an outlier by Mogul will behighlighted in the graph. For rings, the root-mean-square deviation (RMSD) between the ringin question and similar rings identi�ed by Mogul is calculated over all ring torsion angles. If theaverage RMSD is greater than 60 degrees and the minimal RMSD between the ring in question andany Mogul-identi�ed rings is also greater than 60 degrees, then that ring is considered an outlier.The outliers are highlighted in purple. The color gray indicates Mogul did not �nd su�cientequivalents in the CSD to analyse the geometry.
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Ligand 3FI A 1
Bond lengths Bond angles
Torsions Rings
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.
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6 Fit of model and data iO
6.1 Protein, DNA and RNA chains iO
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.
Mol Chain Analysed <RSRZ> #RSRZ>2 OWAB(Å2) Q<0.9
1 A 223/223 (100%) -0.13 7 (3%) 49 44 9, 14, 21, 28 0
All (7) RSRZ outliers are listed below:
Mol Chain Res Type RSRZ1 A 83 GLU 3.31 A 185 VAL 2.91 A 182 GLU 2.91 A 116 TYR 2.31 A 276 ARG 2.21 A 248[A] TYR 2.21 A 183 ASP 2.2
6.2 Non-standard residues in protein, DNA, RNA chains iO
There are no non-standard protein/DNA/RNA residues in this entry.
6.3 Carbohydrates iO
There are no carbohydrates in this entry.
6.4 Ligands iO
In the following table, the Atoms column lists the number of modelled atoms in the group and thenumber de�ned 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 columnlabelled `Q< 0.9' lists the number of atoms with occupancy less than 0.9.
Mol Type Chain Res Atoms RSCC RSR B-factors(Å2) Q<0.93 NA A 305 1/1 0.83 0.20 36,36,36,36 0
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Mol Type Chain Res Atoms RSCC RSR B-factors(Å2) Q<0.94 SCN A 3 3/3 0.91 0.10 23,23,23,27 02 3FI A 1 25/25 0.93 0.12 9,26,31,31 04 SCN A 2 3/3 0.98 0.05 15,15,16,18 0
The following is a graphical depiction of the model �t to experimental electron density of allinstances of the Ligand of Interest. In addition, ligands with molecular weight > 250 and outliersas shown on the geometry validation Tables will also be included. Each �t is shown from di�erentorientation to approximate a three-dimensional view.
Electron density around 3FI A 1:
2mFo-DFc (at 0.7 rmsd) in gray
mFo-DFc (at 3 rmsd) in purple (negative)
and green (positive)
6.5 Other polymers iO
There are no such residues in this entry.
