Newsletter 175
June 30, 2008

The NIH X-Ray Diffraction Interest Group

Newsletter web site: http://mcl1.ncifcrf.gov/nihxray

2008 Gordon Research Conference on Diffraction Methods in Structural Biology
13-18 July 2008, Bates College, Lewiston, ME, USA

21st Congress of the International Union of Crystallography 2008
23 - 31 August 2008, Osaka, Japan

Item 1: May 2008 Publications by Members of the Group


1: Bonifacino JS, Hurley JH.
 Retromer.
Curr Opin Cell Biol. 2008 May 8. PMID: 18472259 
   
2: Batra VK, Beard WA, Shock DD, Pedersen LC, Wilson SH.
 Structures of DNA polymerase beta with active-site 
mismatches suggest a transient abasic site intermediate 
during misincorporation.
Mol Cell. 2008 May 9;30(3):315-24. PMID: 18471977
   
3: Tu C, Tan YH, Shaw G, Zhou Z, Bai Y, Luo R, Ji X.
 Impact of low-frequency hotspot mutation R282Q on the 
structure of p53 DNA-binding domain as revealed by 
crystallography at 1.54 angstroms resolution.
Acta Crystallogr D64(Pt 5):471-7. PMID: 18453682 
   
4: Canagarajah BJ, Hummer G, Prinz WA, Hurley JH.
 Dynamics of cholesterol exchange in the oxysterol binding 
protein family.
J Mol Biol. 2008 May 2;378(3):737-48. PMID: 18377932

Item 2: Tips and Tricks

phenix.refine: crystallographic structure refinement in PHENIX

Pavel V. Afonine, Ralf W. Grosse-Kunstleve, Peter H. Zwart, Thomas C. Terwilliger, Nigel W. Moriarty & Paul D. Adams

A combination of highly efficient programming tools and new or improved crystallographic algorithms provides a very high level of automation and robustness in structure refinement. Their implementation in phenix.refine – state-of-the-art refinement module of PHENIX package – resulted in a complete set of tools that cover most of refinement needs and scenarios, such as: ... (full article).

Pavel V. Afonine's recent lecture on phenix.refine (click here).

Click for Introduction and tips and tricks in Pre-crystallization modification, Crystallization, Post-crystallization treatment, Derivatization, Diffraction, Symmetry, Structure Solution, Structure Refinement, and Structure Analysis & Presentation.

Item 3: Topic Discussion

Click for previous discussions on: Twinning, Low Resolution Crystallography, PHASER, HKL2000, Parallel Protein Expression, Structural Genomics, NCS, Missing Atoms, Trends in Crystallography, and Absorption Correction.

Item 4: Dr. Zbigniew Dauter's Lectures at the NIH (2005)

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"

This site is maintained by Dr. Xinhua Ji (jix@ncifcrf.gov) on the NCI-CCR-MCL server (http://mcl1.ncifcrf.gov).