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International
Tables for Crystallography Volume F Crystallography of biological macromolecules Edited by M. G. Rossmann and E. Arnold © International Union of Crystallography 2006 |
International Tables for Crystallography (2006). Vol. F. ch. 19.5, p. 447
Section 19.5.7.1. Initial models: small unit cells
aWhistler Center for Carbohydrate Research, Purdue University, West Lafayette, IN 47907, USA, and bDepartment of Molecular Biology, Vanderbilt University, Nashville, TN 37235, USA |
For many biopolymers, especially polypeptides, polynucleotides and polysaccharides, the repeating unit is a monomer or a small oligomer and the unit-cell dimensions are in the range 10 to 50 Å. Such unit cells can accommodate one or more polymer helices, packed in an organized fashion.
An initial model is constructed from the primary structure of the repeating unit, using bond lengths, bond angles and some conformation angles derived from surveys of accurate single-crystal analyses. The model must satisfy the observed helical parameters and have reasonable intra- and inter-chain non-bonded, hydrogen-bonded and polar interactions.
This preliminary model provides an approximate solution to the phase problem and a starting point for refinement. Since there is no assurance that the refined model represents the true structure, however, stereochemically plausible alternatives must be carefully considered, refined and objectively adjudicated. Alternatives can include both right- and left-handed helices, single helices, and multistranded helices with parallel and antiparallel strands. The next stage involves the packing arrangement in the unit cell. If two or more helices are present, their positions, orientations and relative polarities must be varied in refinement.
