Page 164 - Macromolecular Crystallography

PHASE REFINEMENT THROUGH DENSITY MODIFICATION 153

Availability: http://www.ysbl.york.ac.uk/ concepts of density modification for the improve-
∼cowtan/pirate/pirate.html ment of phases from crystallography have been
http://www.ccp4.ac.uk implemented in many different programs in the
SHELXE. Part of the SHELX suite of programs, past. Some of the popular density modification
SHELXE uses a variety of novel algorithms to programs implementing the real space restraints dis-
help perform density modification. One of it’s pri- cussed above are SOLOMON (Abrahams, 1997),
maryalgorithmsisthe‘sphere-of-influence’method, DM (Cowtan, 1999), and RESOLVE (Terwilliger,
where a 2.42 Å sphere of 92 (or 272) points is sys- 2003).
tematically moved in real space through the starting
electron density map, regions of high variance are References
assigned to be protein and regions of low variance
are assigned to be solvent. Abrahams, J. P. (1997). Bias reduction in phase refinement
Availability: http://www.uni-ac.gwdg.de/ by modified interference functions: introducing the cor-
SHELX rection. Acta Crystallogr. D 53, 371–376.
Cowtan, K. (1999). Error estimation and bias correction in
phase-improvement calculations. Acta Crystallogr. D 55,
10.10 Conclusions 1555–1567.
Sheldrick, G. M. (2002). Macromolecular phasing with
In this chapter we have presented the concept of
SHELXE. Z. Kristallogr. 217, 644–650.
density modification, where we take a priori infor-
Terwilliger, T. C. (2003). Statistical density modification
mation about the structure of the macromolecule using local pattern matching. Acta Crystallogr. D 59,
we are studying to improve phase estimates. These 1688–1701.