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Protein crystallography for aspiring crystallographers or how to avoid pitfalls and traps in macromolecular structure determination

Published on Nov 1, 2013in FEBS Journal4.739
· DOI :10.1111/febs.12495
Alexander Wlodawer65
Estimated H-index: 65
,
Wladek Minor42
Estimated H-index: 42
+ 1 AuthorsMariusz Jaskolski35
Estimated H-index: 35
(PAN: Polish Academy of Sciences)
Abstract
The number of macromolecular structures deposited in the Protein Data Bank now approaches 100 000, with the vast majority of them determined by crystallographic methods. Thousands of papers describing such structures have been published in the scientific literature, and 20 Nobel Prizes in chemistry or medicine have been awarded for discoveries based on macromolecular crystallography. New hardware and software tools have made crystallography appear to be an almost routine (but still far from being analytical) technique and many structures are now being determined by scientists with very limited experience in the practical aspects of the field. However, this apparent ease is sometimes illusory and proper procedures need to be followed to maintain high standards of structure quality. In addition, many noncrystallographers may have problems with the critical evaluation and interpretation of structural results published in the scientific literature. The present review provides an outline of the technical aspects of crystallography for less experienced practitioners, as well as information that might be useful for users of macromolecular structures, aiming to show them how to interpret (but not overinterpret) the information present in the coordinate files and in their description. A discussion of the extent of information that can be gleaned from the atomic coordinates of structures solved at different resolution is provided, as well as problems and pitfalls encountered in structure determination and interpretation.
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References137
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