wwpdb X-ray Structure Validation Summary Report
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1 wwpdb X-ray Structure Validation Summary Report io Jan 31, :45 PM GMT PDB ID : 1CBS Title : CRYSTAL STRUCTURE OF CELLULAR RETINOIC-ACID-BINDING PROTEINS I AND II IN COMPLEX WITH ALL-TRANS-RETINOIC ACID AND A SYNTHETIC RETINOID Authors : Kleywegt, G.J.; Bergfors, T.; Jones, T.A. Deposited on : Resolution : 1.80 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 at with specic 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-467 Mogul : 1.7 (RC4), CSD as536be (2015) Xtriage (Phenix) : EDS : rb Percentile statistics : v01 (using entries in the PDB archive December 30th 2015) Refmac : CCP4 : Ideal geometry (proteins) : Engh & Huber (2001) Ideal geometry (DNA, RNA) : Parkinson et al. (1996) Validation Pipeline (wwpdb-vp) : trunk26865
2 Page 2 wwpdb X-ray Structure Validation Summary Report 1CBS 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 1.80 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. Metric Whole archive Similar resolution (#Entries) (#Entries, resolution range(å)) R free ( ) Clashscore ( ) Ramachandran outliers ( ) Sidechain outliers ( ) RSRZ outliers ( ) 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 Quality of chain 1 A 137
3 Page 3 wwpdb X-ray Structure Validation Summary Report 1CBS 2 Entry composition io There are 3 unique types of molecules in this entry. The entry contains 1213 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 CELLULAR RETINOIC ACID BINDING PROTEIN TYPE II. Mol Chain Residues Atoms ZeroOcc AltConf Trace 1 A 137 Total C N O S ˆ Molecule 2 is RETINOIC ACID (three-letter code: REA) (formula: C 20 H 28 O 2 ). Mol Chain Residues Atoms ZeroOcc AltConf 2 A 1 Total C O ˆ Molecule 3 is water. Mol Chain Residues Atoms ZeroOcc AltConf 3 A 100 Total O
4 Page 4 wwpdb X-ray Structure Validation Summary Report 1CBS 3 Residue-property plots io These plots are drawn for all protein, RNA and DNA chains in the entry. The rst 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 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: CELLULAR RETINOIC ACID BINDING PROTEIN TYPE II Chain A: P1 N14 M27 L28 R29 V76 K82 S83 V94 C95 L100 T110 L113 D127 E137
5 Page 5 wwpdb X-ray Structure Validation Summary Report 1CBS 4 Data and renement statistics io Property Value Source Space group P Depositor Cell constants 45.65Å 47.56Å 77.61Å a, b, c, α, β, γ Depositor Resolution (Å) Depositor EDS % Data completeness (in resolution range) 90.3 ( ) 90.5 ( ) Depositor EDS R merge (Not available) Depositor R sym (Not available) Depositor < I/σ(I) > (at 1.79Å) Xtriage Renement program X-PLOR Depositor 0.200, Depositor R, R free 0.184, DCC R free test set 1479 reections (10.17%) DCC Wilson B-factor (Å 2 ) 14.8 Xtriage Anisotropy Xtriage Bulk solvent k sol (e/å 3 ), B sol (Å 2 ) 0.40, 72.8 EDS Estimated twinning fraction for k,h,-l Xtriage L-test for twinning 2 < L > = 0.51, < L 2 > = 0.36 Xtriage Outliers 0 of reections Xtriage F o,f c correlation 0.96 EDS Total number of atoms 1213 wwpdb-vp Average B, all atoms (Å 2 ) 16.0 wwpdb-vp Xtriage's analysis on translational NCS is as follows: The largest o-origin peak in the Patterson function is 9.26% of the height of the origin peak. No signicant pseudotranslation is detected. 1 Intensities estimated from amplitudes. 2 Theoretical values of < L >, < L 2 > for acentric reections are 0.5, respectively for untwinned datasets, and 0.333, 0.2 for perfectly twinned datasets.
6 Page 6 wwpdb X-ray Structure Validation Summary Report 1CBS 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: REA 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 A / /1491 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 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 A A A All All 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. The worst 5 of 9 close contacts within the same asymmetric unit are listed below, sorted by their clash magnitude. Interatomic Clash Atom-1 Atom-2 distance (Å) overlap (Å) 1:A:82:LYS:HG2 1:A:100:LEU:HD Continued on next page...
7 Page 7 wwpdb X-ray Structure Validation Summary Report 1CBS Continued from previous page... Atom-1 Atom-2 Interatomic Clash distance (Å) overlap (Å) 2:A:200:REA:H8 2:A:200:REA:H :A:82:LYS:HG2 1:A:100:LEU:CD :A:200:REA:C8 2:A:200:REA:H :A:1:PRO:HB2 1:A:113:LEU:HD There are no symmetry-related clashes. 5.3 Torsion angles io Protein backbone io 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 Percentiles 1 A 135/137 (98%) 132 (98%) 3 (2%) There are no Ramachandran outliers to report Protein sidechains io 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 1 A 123/123 (100%) 120 (98%) 3 (2%) All (3) residues with a non-rotameric sidechain are listed below: Mol Chain Res Type 1 A 14 ASN 1 A 27 MET Continued on next page...
8 Page 8 wwpdb X-ray Structure Validation Summary Report 1CBS Continued from previous page... Mol Chain Res Type 1 A 127 ASP Some sidechains can be ipped to improve hydrogen bonding and reduce clashes. There are no such sidechains identied 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 1 ligand is 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 and the number of bonds (or angles) that are dened in the chemical component dictionary. The Link column lists molecule types, if any, to which the group is linked. 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 > 2 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 Type Chain Res Link Counts RMSZ # Z > 2 Counts RMSZ # Z > 2 2 REA A ,22, (5%) 26,30, (7%) 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 dened in the chemical component dictionary. Similar counts are reported in the Torsion and Rings columns. '-' means no outliers of that kind were identied. Mol Type Chain Res Link Chirals Torsions Rings 2 REA A /13/32/32 0/1/1/1
9 Page 9 wwpdb X-ray Structure Validation Summary Report 1CBS All (1) bond length outliers are listed below: Mol Chain Res Type Atoms Z Observed(Å) Ideal(Å) 2 A 200 REA C1-C All (2) bond angle outliers are listed below: Mol Chain Res Type Atoms Z Observed( o ) Ideal( o ) 2 A 200 REA C11-C10-C A 200 REA C18-C5-C There are no chirality outliers. There are no torsion outliers. There are no ring outliers. 1 monomer is involved in 2 short contacts: Mol Chain Res Type Clashes Symm-Clashes 2 A 200 REA 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.
10 Page 10 wwpdb X-ray Structure Validation Summary Report 1CBS 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 to all X-ray entries and entries of similar resolution. The OWAB column contains the minimum, median, 95 th 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> #RSRZ>2 OWAB(Å 2 ) Q<0.9 1 A 137/137 (100%) , 13, 27, 43 0 There are no RSRZ outliers to report. 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 the number dened in the chemical component dictionary. LLDF column lists the quality of electron density of the group with respect to its neighbouring residues in protein, DNA or RNA chains. The B-factors column lists the minimum, median, 95 th 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 Type Chain Res Atoms RSCC RSR LLDF B-factors(Å 2 ) Q<0.9 2 REA A / ,12,15, Other polymers io There are no such residues in this entry.
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