Improving the scattering-factor formalism in protein refinement: Application of the University at Buffalo Aspherical-Atom Databank to polypeptide structures

Anatoliy Volkov, Marc Messerschmidt, Philip Coppens

Research output: Contribution to journalArticle

67 Citations (Scopus)

Abstract

The University at Buffalo theoretical databank of aspherical pseudoatoms has been tested in the refinement of high-resolution (HR; dmax ≤ 0.44 Å) and truncated 'low-resolution' (LR; dmax = 0.83 Å) X-ray diffraction data sets from the tripeptide Tyr-Gly-Gly monohydrate [Pichon-Pesme et al. (2000), Acta Cryst. B56, 728-737] and hexapeptide cyclo-(d,l-Pro)2-(L-Ala)4 monohydrate [Dittrich et al. (2002), Acta Cryst. B58, 721-727]. Application of the databank to LR data significantly lowers the conventional R factor, improves the determination of bonds and angles to within 0.002-0.003 Å and 0.09-0.17°of the values obtained from a complete multipolar refinement of HR data sets, improves the determination of phase angles by 2-6°compared with the standard independent atom refinement (IAM), removes the majority of the bonding features from the residual Fourier difference maps and improves the atomic displacement parameters (ADPs) and the results of the Hirshfeld rigid-bond test. In the description of the aspherical density from experimental X-ray data, theoretical pseudoatoms were found to perform on the same level as the previously reported experimental databank [Pichon-Pesme et al. (1995), J. Phys. Chem.99, 6242-6250; Jelsch et al. (1998), Acta Cryst. D54, 1306-1318], although no direct comparison of the two methods has been performed. The theoretical databank of aspherical pseudoatoms is shown to be a significant aid in the refinement of accurate experimental X-ray data from large molecular systems, in addition to its use in the reconstruction of molecular densities and the determination of electrostatic interaction energies.

Original languageEnglish (US)
Pages (from-to)160-170
Number of pages11
JournalActa Crystallographica Section D: Biological Crystallography
Volume63
Issue number2
DOIs
StatePublished - Feb 1 2007
Externally publishedYes

Fingerprint

Buffaloes
Databases
Peptides
tyrosyl-glycyl-glycine
Proteins
X-Rays
R Factors
Static Electricity
X-Ray Diffraction
Datasets

Keywords

  • Aspherical scattering factors
  • Aspherical-Atom Databank
  • Multipole refinements
  • Protein refinement

ASJC Scopus subject areas

  • Structural Biology
  • Medicine(all)

Cite this

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title = "Improving the scattering-factor formalism in protein refinement: Application of the University at Buffalo Aspherical-Atom Databank to polypeptide structures",
abstract = "The University at Buffalo theoretical databank of aspherical pseudoatoms has been tested in the refinement of high-resolution (HR; dmax ≤ 0.44 {\AA}) and truncated 'low-resolution' (LR; dmax = 0.83 {\AA}) X-ray diffraction data sets from the tripeptide Tyr-Gly-Gly monohydrate [Pichon-Pesme et al. (2000), Acta Cryst. B56, 728-737] and hexapeptide cyclo-(d,l-Pro)2-(L-Ala)4 monohydrate [Dittrich et al. (2002), Acta Cryst. B58, 721-727]. Application of the databank to LR data significantly lowers the conventional R factor, improves the determination of bonds and angles to within 0.002-0.003 {\AA} and 0.09-0.17°of the values obtained from a complete multipolar refinement of HR data sets, improves the determination of phase angles by 2-6°compared with the standard independent atom refinement (IAM), removes the majority of the bonding features from the residual Fourier difference maps and improves the atomic displacement parameters (ADPs) and the results of the Hirshfeld rigid-bond test. In the description of the aspherical density from experimental X-ray data, theoretical pseudoatoms were found to perform on the same level as the previously reported experimental databank [Pichon-Pesme et al. (1995), J. Phys. Chem.99, 6242-6250; Jelsch et al. (1998), Acta Cryst. D54, 1306-1318], although no direct comparison of the two methods has been performed. The theoretical databank of aspherical pseudoatoms is shown to be a significant aid in the refinement of accurate experimental X-ray data from large molecular systems, in addition to its use in the reconstruction of molecular densities and the determination of electrostatic interaction energies.",
keywords = "Aspherical scattering factors, Aspherical-Atom Databank, Multipole refinements, Protein refinement",
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