Newsletter 155
August 28, 2007


The NIH X-Ray Diffraction Interest Group

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

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

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


Item 1: July 2007 Publications by Members of the Group 

1: Gan J, Wu Y, Prabakaran P, Gu Y, Li Y, Andrykovitch M, Liu H, 
Gong Y, Yan H, Ji X.
 Structural and Biochemical Analyses of Shikimate Dehydrogenase 
AroE from Aquifex aeolicus: Implications for the Catalytic 
Mechanism.
Biochemistry. 2007 Jul 25; PMID: 17649975
   
2: Moon AF, Garcia-Diaz M, Batra VK, Beard WA, Bebenek K, 
Kunkel TA, Wilson SH, Pedersen LC.
 The X family portrait: Structural insights into biological 
functions of X family polymerases.
DNA Repair (Amst). 2007 Jul 11; PMID: 17631059 
   
3: Lin G, Bertolotti-Ciarlet A, Haggarty B, Romano J, McGeehan K, 
Leslie G, d'Oliviere AP, Huang CC, Kwong PD, Doms RW, Hoxie JA.
 Replication competent variants of human immunodeficiency virus 
type-2 lacking the V3 loop exhibit resistance to chemokine 
receptor antagonists.
J Virol. 2007 Jul 3; PMID: 17609282

   
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 Paul Adams' presentation.

Dr. Mark Mayer (NICHD): A Narro 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).