Structural Medicine     

Protein Crystallography Course

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Density modification: theory and practice

This lecture was presented as a powerpoint presentation. To view the slides either use the table of contents below or click here to start

Table of Contents
Density modification: theory and practice
Solvent flattening and NCS averaging: real space
Solvent flattening: real and reciprocal space
NCS averaging and solvent flattening: real space
NCS averaging and solvent flattening: reciprocal space
Solvent flipping: the gamma correction
Translational NCS
Solvent flattening at atomic resolution
Sayre's equation
Sayre's equation at low resolution
Histogram matching
Likelihood and density modification
Detecting NCS
Types of NCS
Defining NCS operators
Domain rotation function
Phased translation function
Defining masks for solvent flattening
Defining masks for averaging
Case history: taq polymerase
Case history: pertussis toxin
Real-space MR for pertussis toxin
Local correlation envelope for pertussis toxin
Case history: Shiga-like toxin B-subunit + trisaccharide

Author: Randy J. Read


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Several of the schematic figures have been adapted from Kleywegt & Read, cited below.

The figure illustrating histogram matching has been adapted from Cowtan & Zhang, also cited below.


Vellieux, F.M.D. & Read, R.J. "Non-crystallographic symmetry averaging in phase refinement and extension", Methods Enzymol. 277: 18-53 (1997).

Kleywegt, G.J. & Read, R.J. "Not your average density", Structure 5: 1557-1569 (1997).

Cowtan, K.D. & Zhang, K.Y.J. "Density modification for macromolecular phase improvement", Prog. Biophys. Mol. Biol. 72: 245-270 (1999).

© 1999-2005 Randy J Read, University of Cambridge. All rights reserved.

Last updated: 7 June, 2005