title: The rate of cis-trans conformation errors is increasing in low-resolution crystal structures.
abstract: Cis-peptide bonds (with the exception of X-Pro) are exceedingly rare in native protein structures, yet a check for these is not currently included in the standard workflow for some common crystallography packages nor in the automated quality checks that are applied during submission to the Protein Data Bank. This appears to be leading to a growing rate of inclusion of spurious cis-peptide bonds in low-resolution structures both in absolute terms and as a fraction of solved residues. Most concerningly, it is possible for structures to contain very large numbers (>1%) of spurious cis-peptide bonds while still achieving excellent quality reports from MolProbity, leading to concerns that ignoring such errors is allowing software to overfit maps without producing telltale errors in, for example, the Ramachandran plot.
authors.affiliation: Institute of Health and Biomedical Innovation, Queensland University of Technology, 60 Musk Avenue, Kelvin Grove, QLD 4059, Australia.
authors.forename: Tristan Ian
authors.initials: TI
authors.lastname: Croll
mesh_terms: D030562:Databases, Protein; D011506:Proteins / Q000737:chemistry*; D013237:Stereoisomerism
chemical_list: D011506:Proteins
keywords: cis-peptide bonds