Structure Validation using Coot Paul Emsley Mar 2007 York University of York

Refinement ValidationExternal e.g. REFMAC Internal Internal External e.g. MolProbity Feature Integration

Validation Tools Geometry Distortion Geometry Distortion Bonds, Angles, Planes Bonds, Angles, Planes B-factor variance B-factor variance Density Fit Density Fit Peptide Omega angle Peptide Omega angle Water check Water check By distance/map density/B-factor By distance/map density/B-factor By difference map variance By difference map variance Un-modelled density blobs Un-modelled density blobs

Stand-alone Tools Coot is designed around a set of libraries Coot is designed around a set of libraries Easy to make “Break-out”/Stand-alone validation tools Easy to make “Break-out”/Stand-alone validation tools Dynarama Dynarama Interactive Ramachandran Tool Interactive Ramachandran Tool Blob identification tool Blob identification tool Density Fit analysis tool Density Fit analysis tool B-factor variation tool B-factor variation tool Nomenclature-fix tool Nomenclature-fix tool

EBI Deposition Validation Tools (GE) “Validation tools used by the EBI are different to Coot tools and give a different set of things about which to be concerned” “Validation tools used by the EBI are different to Coot tools and give a different set of things about which to be concerned” Is this true? Is this true? Does it matter? Does it matter?

Molprobity’s Reduce & Probe

Nomenclature correction (fix-nomenclature-errors 1)

Validation: GLN & ASN B- factor amino-carbonylo outliers Often difficult to decide on the orientation of the last chi angle of GLNs and ASNs Often difficult to decide on the orientation of the last chi angle of GLNs and ASNs (There is geometry-based validation “clique analysis” in REDUCE) (There is geometry-based validation “clique analysis” in REDUCE) This is a complementary (built-in, faster) density- based validation tool This is a complementary (built-in, faster) density- based validation tool Presumes sensible temperature factor refinement Presumes sensible temperature factor refinement Compares the difference in B-factor of OD1 and ND2 with the standard deviation of the B-factors of the other atoms Compares the difference in B-factor of OD1 and ND2 with the standard deviation of the B-factors of the other atoms

GLN and ASN B-factor outliers We choose a value of 2.25 sigma to be the cut-off Even in reference structures there are deviations that result from erroneous structures (presumably) Cut-off for acceptable values Z value Number observed

Validation futures More/Closer integration with Molprobity Tools More/Closer integration with Molprobity Tools Parse REMARKS in Molprobity PDB files Parse REMARKS in Molprobity PDB files Interactive NCS difference graph tool Interactive NCS difference graph tool Communication with Refmac Communication with Refmac Geometric violations Geometric violations Nucleic Acid Validation Nucleic Acid Validation Not any time soon Not any time soon