Tutorial :
Electron Density maps
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 this book and have a look at this excellent
www site 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.
Acknowledgements
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.
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