Once a crystallographer has obtained a diffracting crystal, he collects diffracting data, determine the phases with programs such as those available in the CCP4 suite, and builds an electron density map. Then begins the building of the model, which consists in placing a protein backbone and then amino-acids sidechains into the electron density map. This is done with programs such as O. Then an iterative process of model refinement with programs using energy minimisation such as X-PLOR is performed until a good agreement between the model and the observed data is obtained.
If you want to know more about crystallography (for teaching purposes or just to increase your general awareness), you should seriously consider reading Gale Rhode's book "Crystallography made crystal clear" and have a look at Bernhard Rupp's excellent "Crystallography101" that explain aspects of crystallography in great detail.
In this tutorial, we'll have a look at two proteins and their corresponding electron density map. It is advisable to complete both tutorials and start with the fatty acid binding protein. Then, we will learn how to fit residues into the density given a backbone fragment, a map, and the sequence of the protein to solve.
I wish to thank:
Prof. Gale Rhodes for all the work he has done in making contacts to obtain electron density maps that I could use in this tutorial; for his general enthusiasm, for his excellent suggestions, for the general testing of the Mac version.
Dr. Nate Winter for all the work he has done in making contacts to obtain electron density maps that I could use in this tutorial.
Dr. Jim Thompson, Dr. Nate Winter, and Prof. Len Banaszak for having provided coordinates and electronic density map of the liver fatty-acid binding protein and allowed me to make them publicly available for this tutorial.
Dr. Doug Ohlendorf for having provided a lysozyme data set to Dr Nate Winter who did a rigid body refinement of the coordinates deposited by K.P. Wilson, B.A. Malcom and B.W.Matthews (pdb entry 1hel) to Doug Ohlendorf's data set.
Dr. Alwyn Jones for having let me use the DN6 electron density file format and for having granted me access to the source code of MAPPAGE (a program that converts X-PLOR huge text electron density maps to the much more compact format used by O). It has avoided me to invent yet an other electron density map file format.
Dr. Jeff Shaw and Mark Rould for their help getting me into the crystallography world and for their help in understanding what was requested to generate electron density maps with X-PLOR.