Newsletter 158
October 8, 2007


The NIH X-Ray Diffraction Interest Group

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

Advances in Protein Crystallography
23 - 24 January 2008, Palm Springs, CA, USA

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

   

Item 1: September 2007 Publications by Members of the Group 

1: Hosseinpour F, Timsit Y, Koike C, Matsui K, Yamamoto Y, Moore R, 
Negishi M.
 Overexpression of the Rho-guanine nucleotide exchange factor ECT2 
inhibits nuclear translocation of nuclear receptor CAR in the mouse 
liver.
FEBS Lett. 2007 Sep 21; PMID: 17904126 
   
2: Huang CC, Lam SN, Acharya P, Tang M, Xiang SH, Hussan SS, Stanfield
RL, Robinson J, Sodroski J, Wilson IA, Wyatt R, Bewley CA, Kwong PD.
 Structures of the CCR5 N terminus and of a tyrosine-sulfated antibody
with HIV-1 gp120 and CD4.
Science. 317(5846):1930-4. PMID: 17901336
   
3: Yang W, Woodgate R.
 What a difference a decade makes: Insights into translesion DNA 
synthesis.
Proc Natl Acad Sci U S A. 104(40):15591-8. PMID: 17898175
   
4: Gustchina E, Louis JM, Lam SN, Bewley CA, Clore GM.
 A Monoclonal Fab Derived From a Human Non-Immune Phage Library Reveals
a New Epitope on gp41 and Neutralizes Diverse HIV-1 Strains.
J Virol. 2007 Sep 26; PMID: 17898046
   
5: Biertumpfel C, Yang W, Suck D.
 Crystal structure of T4 endonuclease VII resolving a Holliday junction.
Nature. 449(7162):616-20. PMID: 17873859
   
6: Prasad R, Liu Y, Deterding LJ, Poltoratsky VP, Kedar PS, Horton JK,
Kanno S, Asagoshi K, Hou EW, Khodyreva SN, Lavrik OI, Tomer KB, Yasui 
A, Wilson SH.
 HMGB1 is a cofactor in mammalian base excision repair.
Mol Cell. 27(5):829-41. PMID: 17803946
   
7: Xie H, Ng D, Savinov SN, Dey B, Kwong PD, Wyatt R, Smith AB 3rd, 
Hendrickson WA.
 Structure-Activity Relationships in the Binding of Chemically 
Derivatized CD4 to gp120 from Human Immunodeficiency Virus.
J Med Chem. 50(20):4898-4908. PMID: 17803292

Item 2: Tips and Tricks

Dr. Alla Gustchina (NCI): I'd like to share the link to a very useful website with examples of making publication quality figures by using PyMol, which I learned from my friend. I hope that link will be helpful to anybody if needed.
http://137.189.50.96/kbwong/teaching/pymol/pymol_tutorial.html

Item 3: Topic Discussion - Twinning

Please share your experience in twinning by presenting a case study. To learn or to review the basics of twinning, see CCP4 General and Paul Adams' presentation.

Dr. Mark Mayer (NICHD): A Narrow Escape from Merohedral Twinning 

    Merohedral twinning is a special form of disorder that most crystallographers will be forced to deal with at some point in their career. It is different from twinning which arises when crystals fuse during growth, which is easily recognized either in the light microscope, or from diffraction images which reveal the presence of more than one lattice. In the case of merohedral twinning, the crystal contains microdomains in which the same lattice is present but in different orientations related by a twinning operator. As a result, the observed intensities are not accurate, in the sense that they arise from the sum of the unrelated intensities of the twin components. Because the intensities do not correspond to those generated by a single lattice, refinement stalls at unreasonably high R values, and in some cases the structure cannot be solved at all. (Full Article)


Dr. Lothar Esser (NCI): Refinement in Case of Twinning 

    Despite working in crystallography for a number of years, it was only recently that I was asked to refine a structure against twinned data. The unfinished structure was handed to me after the post-doc who had been working on this project had left the lab. The crystal diffracted x-rays to 2.2 Ǻ with intensities obeying the symmetry of space group R3. The structure was solved by molecular replacement before it was recognized that the crystal was twinned using a model of > 99% sequence identity. As the refinement did not progress as it should, it became clear that the data were twinned. Merohedral twinning in R3 is quite common and the extra 2 fold axis, that generates the twin domain, relates reflection indices of h, k, l to k, h, -l. Having no prior experience with the refinement of structures against twinned data, I tried all programs that were available to me.(Full Article)

Click for previous discussions on: 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).