Introduction and validation of an invariom database for amino-acid, peptide and protein molecules

• Published in: Acta crystallographica. Section D, Biological crystallography. Biological crystallography., 2006-11, Vol.62 (11), p.1325-1335
• Main Authors: Luger, P., Hübschle, C. B., Spackman, M. A., Dittrich, B.
• Format: Article
• Language: English
• Subjects: Amino Acids - chemistry; Databases, Protein; invariom database; Models, Molecular; Peptides - chemistry; Proteins - chemistry; structural refinement; Structure-Activity Relationship
• ISSN: 1399-0047; 0907-4449; 1399-0047
• DOI: 10.1107/S090744490602899X

A database of invarioms for structural refinement of amino‐acid, oligopeptide and protein molecules is presented. The spherical scattering factors of the independent atom or promolecule model are replaced by `individual' aspherical scattering factors that take into account the chemical environment of a bonded atom. All amino acids were analysed in terms of their invariom fragments. In order to generate 73 database entries that cover this class of compounds, 37 model compounds were geometry‐optimized and theoretical structure factors were calculated. Multipole refinements were then performed on these theoretical structure factors to yield the invariom database. Validation of this database on an extensive number of experimental small‐molecule crystal structures of varying quality and resolution shows that invariom modelling improves various figures of merit. Differences in figures of merit between invariom and promolecule models give insight into the importance of disorder for future protein‐invariom refinements. The suitability of structural data for application of invarioms can be predicted by Cruickshank's diffraction‐component precision index [Cruickshank (1999), Acta Cryst. D55, 583–601].