Newsletter 189
 February 23, 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: January 2009 Publications by Members of the Group 

1: Lu G, Dolgner SJ, Hall TM.
 Understanding and engineering RNA sequence specificity of PUF proteins.
Curr Opin Struct Biol. 2009 Jan 29. PMID: 19186050 
   
2: Castillo-Acosta VM, Ruiz-Pérez LM, Yang W, González-Pacanowska D, Vidal AE.
 Identification of a residue critical for the excision of 3'-blocking ends in
apurinic/apyrimidinic endonucleases of the Xth family.
Nucleic Acids Res. 2009 Jan 30. PMID: 19181704 
   
3: Lountos GT, Tropea JE, Zhang D, Jobson AG, Pommier Y, Shoemaker RH, Waugh DS.
 Crystal structure of checkpoint kinase 2 in complex with NSC 109555, a potent and
selective inhibitor.
Protein Sci. 2009 Jan;18(1):92-100. PMID: 19177354 
   
4: Jenkins LM, Yamaguchi H, Hayashi R, Cherry S, Tropea JE, Miller M, Wlodawer A,
Appella E, Mazur SJ.
 Two Distinct Motifs within the p53 Transactivation Domain Bind to the Taz2 Domain
of p300 and Are Differentially Affected by Phosphorylation (dagger).
Biochemistry. 2009 Jan 23. PMID: 19166313 
   
5: Tropea JE, Cherry S, Waugh DS.
 Expression and purification of soluble His(6)-tagged TEV protease.
Methods Mol Biol. 2009;498:297-307. PMID: 18988033 
   
6: Austin BP, Nallamsetty S, Waugh DS.
 Hexahistidine-tagged maltose-binding protein as a fusion partner for the
production of soluble recombinant proteins in Escherichia coli.
Methods Mol Biol. 2009;498:157-72. PMID: 18988025

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?

       

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).