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On the application of an experimental multipolar pseudo‐atom library for accurate refinement of small‐molecule and protein crystal structures

On the application of an experimental multipolar pseudo‐atom library for accurate refinement of... With an increasing number of biomacromolecular crystal structures being measured to ultra‐high resolution, it has become possible to extend to large systems experimental charge‐density methods that are usually applied to small molecules. A library has been built of average multipole populations describing the electron density of chemical groups in all 20 amino acids found in proteins. The library uses the Hansen & Coppens multipolar pseudo‐atom model to derive molecular electron density and electrostatic potential distributions. The library values are obtained from several small peptide or amino acid crystal structures refined against ultra‐high‐resolution X‐ray diffraction data. The library transfer is applied automatically in the MoPro software suite to peptide and protein structures measured at atomic resolution. The transferred multipolar parameters are kept fixed while the positional and thermal parameters are refined. This enables a proper deconvolution of thermal motion and valence‐electron‐density redistributions, even when the diffraction data do not extend to subatomic resolution. The use of the experimental library multipolar atom model (ELMAM) also has a major impact on crystallographic structure modelling in the case of small‐molecule crystals at atomic resolution. Compared to a spherical‐atom model, the library transfer results in a more accurate crystal structure, notably in terms of thermal displacement parameters and bond distances involving H atoms. Upon transfer, crystallographic statistics of fit are improved, particularly free R factors, and residual electron‐density maps are cleaner. http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png Acta Crystallographica Section A Foundations of Crystallography Wiley

On the application of an experimental multipolar pseudo‐atom library for accurate refinement of small‐molecule and protein crystal structures

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References (37)

Publisher
Wiley
Copyright
Copyright © 2007 Wiley Subscription Services, Inc., A Wiley Company
ISSN
0108-7673
eISSN
1600-5724
DOI
10.1107/S0108767306053748
pmid
17301471
Publisher site
See Article on Publisher Site

Abstract

With an increasing number of biomacromolecular crystal structures being measured to ultra‐high resolution, it has become possible to extend to large systems experimental charge‐density methods that are usually applied to small molecules. A library has been built of average multipole populations describing the electron density of chemical groups in all 20 amino acids found in proteins. The library uses the Hansen & Coppens multipolar pseudo‐atom model to derive molecular electron density and electrostatic potential distributions. The library values are obtained from several small peptide or amino acid crystal structures refined against ultra‐high‐resolution X‐ray diffraction data. The library transfer is applied automatically in the MoPro software suite to peptide and protein structures measured at atomic resolution. The transferred multipolar parameters are kept fixed while the positional and thermal parameters are refined. This enables a proper deconvolution of thermal motion and valence‐electron‐density redistributions, even when the diffraction data do not extend to subatomic resolution. The use of the experimental library multipolar atom model (ELMAM) also has a major impact on crystallographic structure modelling in the case of small‐molecule crystals at atomic resolution. Compared to a spherical‐atom model, the library transfer results in a more accurate crystal structure, notably in terms of thermal displacement parameters and bond distances involving H atoms. Upon transfer, crystallographic statistics of fit are improved, particularly free R factors, and residual electron‐density maps are cleaner.

Journal

Acta Crystallographica Section A Foundations of CrystallographyWiley

Published: Mar 1, 2007

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