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.
• To introduce some of the concepts in macromolecular NMR spectroscopy.
• To raise some of the issues that structural bioinformaticians should be aware of when working with structures determined by NMR spectroscopy.
• To introduce the ways in which the stereochemical quality of a protein structure can be assessed.

Objectives

After this lecture you will:

• be aware of X-ray crystallography as a technique for macromolecular structure determination;
• be aware of nuclear magnetic resonance spectroscopy as a technique for macromolecular structure determination;
be familiar with the criteria that are used in assessing the stereochemical quality of a protein.

Supplementary Material

The course Structural biochemistry (KBB056) contains more extensive material on both X-ray crystallography and NMR spectroscopy.

There are many excellent eductional resources on X-ray crystallography, including:

• A Glossary of Terms from Crystallography, NMR, and Homology Modeling by Gale Rhodes
• Protein Crystallography Course at the University of Cambridge, particularly
  • Overview of macromolecular X-ray crystallography by Randy Read
  • Introduction to fitting, refinement and validation by Randy Read
  • Fitting, Refinement & Validation by Phil Evans
• A Brief Introduction to Protein Crystallography by Dave Lawson
• Crystallography 101 by Bernhard Rupp
• A Non-Mathematical Introduction to X-ray Diffraction by Charles A. Taylor
• Book of Fourier by Kevin Cowtan

Wikipedia contains an overview of protein nuclear magnetic resonance spectroscopy.

PROCHECK results and various other information about each Protein Data Bank entry are given in PDBsum. I recommend that you read the descriptions of the checks performed by PROCHECK, and that you look at some of the sample output produced by that program.