Newsletter 190
 March 9, 2009


The NIH X-Ray Diffraction Interest Group

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

2009 Mid-Atlantic Macromolecular Crystallography Meeting (05/28-30)

2009 Meeting of American Crystallographic Association (07/25-30)

Item 1: February 2009 Publications by Members of the Group 

1: Li YF, Poole S, Rasulova F, McVeigh AL, Savarino SJ, Xia D.
 Crystallization and preliminary X-ray diffraction analyses of several forms of
the CfaB major subunit of enterotoxigenic Escherichia coli CFA/I fimbriae.
Acta Crystallogr F. 2009 Mar 1;65(Pt 3):242-7. PMID: 19255474
   
2: Pasek M, Ramakrishnan B, Boeggeman E, Manzoni M, Waybright TJ, Qasba PK.
 Bioconjugation and Detection of Lactosamine Moiety using
alpha1,3-Galactosyltransferase Mutants That Transfer C2-Modified Galactose with a
Chemical Handle.
Bioconjug Chem. 2009 Feb 26. PMID: 19245254
   
3: Prasad R, Longley MJ, Sharief FS, Hou EW, Copeland WC, Wilson SH.
 Human DNA polymerase {theta} possesses 5'-dRP lyase activity and functions in
single-nucleotide base excision repair in vitro.
Nucleic Acids Res. 2009 Feb 2. PMID: 19188258 
   
4: Lountos GT, Austin BP, Nallamsetty S, Waugh DS.
 Atomic resolution structure of the cytoplasmic domain of Yersinia pestis YscU, a 
regulatory switch involved in type III secretion.
Protein Sci. 2009 Feb;18(2):467-74. PMID: 19165725 
   
5: Hurley JH, Im YJ, Lee HH, Ren X, Wollert T, Yang D.
 Piecing together the ESCRTs.
Biochem Soc Trans. 2009 Feb;37(Pt 1):161-6. Review. PMID: 19143623

Item 2: Tips and Tricks

Item 3: Topic Discussion - Test Set and R-free

Editor: Please share your practice and theory on Test Set and R-free with fellow members of the group. A list of suggested subtopics is shown below. 

 

(1) How many reflections do you put in Test Set for R-free calculations, a centerin percentage or a certain number?

(2) For isomorphous structures, such as a wild type and several mutant structures crystallized in the same lattice, do you use the same Test Set for all these structures?

(3) Do you use the same Test Set if you re-process your data during refinement or obtain a better data set?

(4) Do you use the same Test Set when you switch refinement programs?

(5) What do you do to the Test Set if you find out the crystal is twinned during refinement without twinning considerations?

(6) Do you include some or all data in the Test Set for the final rounds of refinement?

      
Mark Mayer: How about an addition?

(7) When you have NCS do you pick Test Set using thin shells?

     

Click for previous discussions on: Validation, 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).