Newsletter 137
December 18, 2006

The NIH X-Ray Diffraction Interest Group

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

Advances in Protein Crystallography 24 - 25 January 2007, South San Francisco, CA, USA

9th International Conference on Biology and Synchrotron Radiation 13-17 August 2007, Manchester, England

Item 1: November 2006 Publications by Members:

 1:  Miller M. 
 Phospho-Dependent Protein Recognition Motifs Contained in 
C/EBP Family of Transcription Factors: in Silico Studies.
Cell Cycle. 2006 Nov 1;5(21)PMID: 17102635 
  
2:  Ziolkowska NE, Wlodawer A. 
 Structural studies of algal lectins with anti-HIV activity.
Acta Biochim Pol. 2006 Nov 27; PMID: 17128290 
  
3:  Poltoratsky V, Prasad R, Horton JK, Wilson SH. 
 Down-regulation of DNA polymerase beta accompanies somatic 
hypermutation in human BL2 cell lines.
DNA Repair (Amst). 2006 Nov 24; PMID: 17127106 
   
4:  Horton JK, Wilson SH. 
 Hypersensitivity phenotypes associated with genetic and 
synthetic inhibitor-induced base excision repair deficiency.
DNA Repair (Amst). 2006 Nov 17; PMID: 17113833 
   
5:  Saikh KU, Kissner TL, Dyas B, Tropea JE, Waugh DS, 
Ulrich RG. 
 Human Cytolytic T Cell Recognition of Yersinia pestis 
Virulence Proteins That Target Innate Immune Responses.
J Infect Dis. 2006 Dec 15;194(12):1753-60. PMID: 17109349 
   
6:  Batra VK, Shock DD, Prasad R, Beard WA, Hou EW, Pedersen 
LC, Sayer JM, Yagi H, Kumar S, Jerina DM, Wilson SH. 
 Structure of DNA polymerase beta with a 
benzo[c]phenanthrene diol epoxide-adducted template 
exhibits mutagenic features.
Proc Natl Acad Sci U S A. 2006 Nov 14;103(46):17231-6. 
PMID: 17079493 
   
7:  Hurley JH, Lee S, Prag G. 
 Ubiquitin-binding domains.
Biochem J. 2006 Nov 1;399(3):361-72. Review. PMID: 17034365

Item 2: Tips and Tricks - Lysine Methylation

Xinhua Ji (NCI):It appears that lysine methylation should be considered a routine step not only in traditional (low-throughput) crystallization trials but also for structural genomics (high-throughput) attempts. Walter and co-workers outlined a detailed protocol with ten examples in their recent article (Structure 14:1617-1622, 2006). The protocol was derived from previously published method by Rayment and co-workers (Science 261:50-58, 1993) and Rayment (Methods Enzymol. 276:171-179, 1997). A recent success within the NIH X-ray Diffraction Group was reported by Schubot and Waugh (Acta Cryst. D60:1981-1986, 2004), showing that the method was pivotal in the de novo crystallization of a ternary complex that contains three protein molecules!

Click for Introduction and tips and tricks in Crystallization, Post-crystallization treatments, Derivatization, Diffraction, Symmetry, Structure Solution, Structure Refinement, and Structure Analysis.

Item 3: Topic Discussion

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

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).