Computational methods in bioinformatics (2014-2015)
Lecture 5
Macromolecular structure determination by X-ray crystallography
Aims
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To introduce some of the concepts in macromolecular X-ray crystallography.
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To raise some of the issues that structural bioinformaticians should be
aware of when working with structures determined by X-ray crystallography.
Objectives
After this lecture you will be able to:
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describe how electron density maps are represented;
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implement an algorithm for skeletonizing an electron density map;
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describe how an alpha-carbon trace can be constructed;
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discuss concepts related to model quality of X-ray structures;
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discuss difficulties in interpreting X-ray structures.
Supplementary Material
Some of the lecture slides are available on-line
(PDF).
Articles mentioned in the lecture include:
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J. Greer (1974)
Three-dimensional pattern recognition: An approach to automated
interpretation of electron density maps of proteins.
J. Mol. Biol., 82279-301.
doi:10.1016/0022-2836(74)90591-9
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J. M. Word, S. C. Lovell, J. S. Richardson and D. C. Richardson (1998)
Asparagine and glutamine: using hydrogen atom contacts in the choice of
side-chain amide orientation.
J. Mol. Biol., 285, 173-1747.
doi:10.1006/jmbi.1998.2401
Before the next lecture pleae look at:
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R. J. Morris, A. Perrakis and V. S. Lamzin (2002)
ARP/wARP's model-building algorithms. I. The main chain.
Acta Cryst., D58, 968-974.
doi:10.1107/S0907444902005462
There are many excellent eductional resources on X-ray crystallography,
including:
Last Modified: 19 November 2014
by Graham Kemp