Newsletter 178
September 8, 2008

The NIH X-Ray Diffraction Interest Group

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

Item 1: August 2008 Publications by Members of the Group

1: Kim YC, Tang C, Clore GM, Hummer G.
 Replica exchange simulations of transient encounter complexes in
protein-protein association.
Proc Natl Acad Sci U S A. 2008 Aug 26. PMID: 18728193
   
2: Singh K, Gittis AG, Nguyen P, Gowda DC, Miller LH, Garboczi DN.
 Structure of the DBL3x domain of pregnancy-associated malaria 
protein VAR2CSA complexed with chondroitin sulfate A.
Nat Struct Mol Biol. 2008 Aug 24. PMID: 18724365
   
3: Kedar PS, Stefanick DF, Horton JK, Wilson SH.
 Interaction between PARP-1 and ATR in mouse fibroblasts is blocked
by PARP inhibition.
DNA Repair (Amst). 2008 Aug 21. PMID: 18691676
   
4: Pletnev S, Shcherbo D, Chudakov D, Pletneva N, Merzlyak E, 
Wlodawer A, Dauter Z, Pletnev V.
 A crystallographic study of bright far-red fluorescent protein 
mKate reveals pH-induced cis-trans isomerization of the chromophore.
J Biol Chem. 2008 Aug 4. PMID: 18682399
   
5: Ji X, Pal A, Kalathur R, Hu X, Gu Y, Saavedra JE, Buzard GS, 
Srinivasan A, Keefer L, Singh SV.
 Structure-based design of anticancer prodrug PABA/NO.
Drug Design, Development and Therapy. 2008:2 123-130.

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).