TY - JOUR
T1 - Improving the scattering-factor formalism in protein refinement
T2 - Application of the University at Buffalo Aspherical-Atom Databank to polypeptide structures
AU - Volkov, Anatoliy
AU - Messerschmidt, Marc
AU - Coppens, Philip
PY - 2007/2
Y1 - 2007/2
N2 - 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.
AB - 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.
KW - Aspherical scattering factors
KW - Aspherical-Atom Databank
KW - Multipole refinements
KW - Protein refinement
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U2 - 10.1107/S0907444906044453
DO - 10.1107/S0907444906044453
M3 - Article
C2 - 17242509
AN - SCOPUS:33846661069
SN - 0907-4449
VL - 63
SP - 160
EP - 170
JO - Acta Crystallographica Section D: Biological Crystallography
JF - Acta Crystallographica Section D: Biological Crystallography
IS - 2
ER -