Computational methods in bioinformatics (2017-2018)
Lecture 4
Macromolecular structure determination by X-ray crystallography
Aims
-
To introduce some of the concepts in macromolecular X-ray crystallography.
-
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:
-
describe how electron density maps are represented;
-
implement an algorithm for skeletonizing an electron density map;
-
describe how an alpha-carbon trace can be constructed;
-
discuss concepts related to model quality of X-ray structures;
-
discuss difficulties in interpreting X-ray structures.
Supplementary Material
Some of the lecture slides are available on-line
(1 per page,
4 per page,
local scanned copy).
Articles mentioned in the lecture include:
-
J. Greer (1974)
Three-dimensional pattern recognition: An approach to automated
interpretation of electron density maps of proteins.
J. Mol. Biol., 82, 279-301.
doi:10.1016/0022-2836(74)90591-9
-
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
There are many excellent eductional resources on X-ray crystallography,
including:
Last Modified: 3 December 2017
by Graham Kemp