A priori
             chemical information

Brunger, A. T.; Adams, P. D.; Rice, L. M.

doi:10.1107/97809553602060000694

International
Tables for
Crystallography
Volume F
Crystallography of biological macromolecules
Edited by M. G. Rossmann and E. Arnold

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International Tables for Crystallography (2006). Vol. F. ch. 18.2, p. 377 | 1 | 2 |

Section 18.2.3.2. A priori chemical information

A. T. Brunger,^a ^* P. D. Adams^b and L. M. Rice^c

^a The Howard Hughes Medical Institute, and Departments of Molecular and Cellular Physiology, Neurology and Neurological Sciences, and Stanford Synchrotron Radiation Laboratory, Stanford Universty, 1201 Welch Road, MSLS P210, Stanford, CA 94305-5489, USA,^bThe Howard Hughes Medical Institute and Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA, and ^cDepartment of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA
Correspondence e-mail: axel.brunger@stanford.edu

18.2.3.2. A priori chemical information

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The parameters for the covalent terms in $[E_{\rm chem}]$ [equation (18.2.3.1)] can be derived from the average geometry and (r.m.s.) deviations observed in a small-molecule database. Extensive statistical analyses were undertaken for the chemical moieties of proteins (Engh & Huber, 1991) and polynucleotides (Parkinson et al., 1996) using the Cambridge Structural Database (Allen et al., 1983). Analysis of the ever-increasing number of atomic resolution macromolecular crystal structures will no doubt cause some modifications of these parameters in the future.

It is common to use a purely repulsive quartic function $[(E_{\rm repulsive})]$ for the non-bonded interactions that are included in $[E_{\rm chem}]$ (Hendrickson, 1985): $[E_{\rm repulsive} = \textstyle{\sum\limits_{ij}} [(cR_{ij}^{\min})^{n} - R_{ij}^{n}]^{m}, \eqno(18.2.3.10)]$ where $[R_{ij}]$ is the distance between two atoms i and j, $[R_{ij}^{\min}]$ is the van der Waals radius for a particular atom pair ij, $[c \leq 1]$ is a constant that is sometimes used to reduce the radii, and n = 2, m = 2 or n = 1, m = 4. van der Waals attraction and electrostatic interactions are usually not included in crystallographic refinement. These simplifications are valid since the diffraction data contain information that is able to produce atomic conformations consistent with actual non-bonded interactions. In fact, atomic resolution crystal structures can be used to derive parameters for electrostatic charge distributions (Pearlman & Kim, 1990).

References

Allen, F. H., Kennard, O. & Taylor, R. (1983). Systematic analysis of structural data as a research technique in organic chemistry. Acc. Chem. Res. 16, 146–153.Google Scholar

Engh, R. A. & Huber, R. (1991). Accurate bond and angle parameters for X-ray structure refinement. Acta Cryst. A47, 392–400.Google Scholar

Hendrickson, W. A. (1985). Stereochemically restrained refinement of macromolecular structures. Methods Enzymol. 115, 252–270.Google Scholar

Parkinson, G., Vojtechovsky, J., Clowney, L., Brunger, A. T. & Berman, H. M. (1996). New parameters for the refinement of nucleic acid-containing structures. Acta Cryst. D52, 57–64.Google Scholar

Pearlman, D. A. & Kim, S.-H. (1990). Atomic charges for DNA constituents derived from single-crystal X-ray diffraction data. J. Mol. Biol. 211, 171–187.Google Scholar

International Tables for Crystallography (2006). Vol. F. ch. 18.2, p. 377