e16.html

Part 1: "How to read international tables?"

Part 2: "Data collection strategy" and "Twinning"

"Phasing methods - a general introduction to all methods"

Part 3: "SAD phasing, Quick halide soaking, and Radiation damage

with possible use of it for phasing"

1: Bell JK, Botos I, Hall PR, Askins J, Shiloach J, Segal DM, Davies DR.
The molecular structure of the Toll-like receptor 3 ligand-binding domain.
Proc Natl Acad Sci U S A. 2005 Jul 25; PMID: 16043704

2: Hickman AB, Perez ZN, Zhou L, Musingarimi P, Ghirlando R, Hinshaw JE, Craig NL, Dyda F.
Molecular architecture of a eukaryotic DNA transposase.
Nat Struct Mol Biol. 2005 Jul 24; [Epub ahead of print] PMID: 16041385

3: Lee K, Boovanahalli SK, Nam KY, Kang SU, Lee M, Phan J, Wu L, Waugh DS, Zhang ZY, No KT, Lee JJ, Burke TR Jr.
Synthesis of tripeptides as potent Yersinia protein tyrosine phosphatase
inhibitors.
Bioorg Med Chem Lett. 2005 Jul 19; PMID: 16039123

4: Laronde-Leblanc N, Guszczynski T, Copeland T, Wlodawer A.
Structure and activity of the atypical serine kinase Rio1.
FEBS J. 2005 Jul;272(14):3698-713. PMID: 16008568

5: Nowotny M, Gaidamakov SA, Crouch RJ, Yang W.
Crystal structures of RNase H bound to an RNA/DNA hybrid: substrate specificity and metal-dependent catalysis.
Cell. 2005 Jul 1;121(7):1005-16. PMID: 15989951

6: Dauter Z, Botos I, LaRonde-LeBlanc N, Wlodawer A.
Pathological crystallography: case studies of several unusual macromolecular crystals.
Acta Crystallogr D Biol Crystallogr. 2005 Jul;61(Pt 7):967-75. PMID: 15983420

7: Gurung B, Yu L, Xia D, Yu CA.
The iron-sulfur cluster of the rieske iron-sulfur protein functions as a
proton-exiting gate in the cytochrome bc(1) complex.
J Biol Chem. 2005 Jul 1;280(26):24895-902. PMID: 15878858

8: Prasanna MD, Vondrasek J, Wlodawer A, Bhat TN.
Application of InChI to curate, index, and query 3-D structures.
Proteins. 2005 Jul 1;60(1):1-4. PMID: 15861385

PHASER: MR with Maximum Likelihood

Dr. Mark Mayer (NICHD): Keeping up with new software is time consuming especially for small labs. The NIH X-Ray Diffraction Interest Group News Letter gives us a chance as a community to share information about newer programs, and tips for using them. On the Mac side of things the Structural Biology Grid has version of CNS and Refmac that support multithreading and fast FFT calculations on G4/G5 systems which significantly speed up calculation of composite omit maps. The binaries are available from: http://www.sbgrid.org/osx.php?software=1&id=0

A relatively new Molecular Replacement program PHASER has just been updated to version 1.3.1 and appears to be a very useful tool.

PHASER was written by Randy Read, Ralf Grosse-Kunstleve and colleagues as part of PHENIX and is available from: http://www-structmed.cimr.cam.ac.uk/phaser/.

Binaries are available for multiple platforms including Mac OsX, linux, SGIs, and PCs. An interface to CCP4i is also available. Eventually the program will be incorporated into the CCP4 suite.

Among many nice features are use of maximum likelihood targets; anisotropy correction; a very user friendly interface when run from CCP4i; Z scoring as an indication of the success of the fit; automatic testing of enantiomorphic space groups; the ability to use an ensemble of models as targets; and the ability to search for and fit domains independently. The latter feature was attractive to me in the case of a 2.2-angstrom data set from my home facility (P4₁2₁2 or P4₃2₁2) for which I was expecting a large conformational change from my search model. PHASER identified the space group and found the two domains in their new orientations without intervention.

The program has many features I have not tried which extend those available in MOLREP and AmoRe. Perhaps this is a topic for discussion?