Newsletter 94
April 25, 2005


The NIH X-Ray Diffraction Interest Group

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

Item 1: Local Meetings and Seminars

 
1. The 35th Mid-Atlantic Crystallography Meeting <http://www.niaid.nih.gov/dir/labs/lig/crystal/default.asp> May 11-13.

2. The NIH meeting "Structural Analysis of Large Macromolecular Assemblies: Sizing Up the Challenges" <http://pub.nigms.nih.gov/generic_meeting/index.cfm?id=7> June 2-3.

 

Item 2: March 2005 Publications by Members:

 

1:  Williams DC Jr, Cai M, Suh JY, Peterkofsky A, Clore GM.
Solution NMR structure of the 48 kDa IIAmannose-HPr complex of the Escherichia coli mannose phosphotransferase system.
J Biol Chem. 2005 Mar 23; [Epub ahead of print] PMID: 15788390

2:  Su HP, Garman SC, Allison TJ, Fogg C, Moss B, Garboczi DN.
The 1.51-A structure of the poxvirus L1 protein, a target of potent neutralizing antibodies.
Proc Natl Acad Sci U S A. 2005 Mar 22;102(12):4240-5. PMID: 15761054

3:  Mayer ML.
Some assembly required.
Nat Struct Mol Biol. 2005 Mar;12(3):208-9. PMID: 15744319

4:  Ramakrishnan B, Boeggeman E, Qasba PK.
Mutation of arginine 228 to lysine enhances the glucosyltransferase activity of bovine beta-1,4-galactosyltransferase I.
Biochemistry. 2005 Mar 8;44(9):3202-10. PMID: 15736931

5:  Caldovic L, Morizono H, Panglao MG, Lopez GY, Shi D, Summar ML, Tuchman M.
Late onset N-acetylglutamate synthase deficiency caused by hypomorphic alleles.
Hum Mutat. 2005 Mar;25(3):293-8. PMID: 15714518

6:  Schubot FD, Jackson MW, Penrose KJ, Cherry S, Tropea JE, Plano GV, Waugh DS.
Three-dimensional structure of a macromolecular assembly that regulates type III secretion in Yersinia pestis.
J Mol Biol. 2005 Mar 4;346(4):1147-61. PMID: 15701523

7:  Tang C, Williams DC Jr, Ghirlando R, Clore GM.
Solution structure of enzyme IIA(Chitobiose) from the N,N'-diacetylchitobiose branch of the Escherichia coli phosphotransferase system.
J Biol Chem. 2005 Mar 25;280(12):11770-80. PMID: 15654077

8:  Gong X, Yu L, Xia D, Yu CA.
Evidence for electron equilibrium between the two hemes bL in the dimeric cytochrome bc1 complex.
J Biol Chem. 2005 Mar 11;280(10):9251-7. PMID: 15615714


Item 3: Tips and Tricks

This section is always open for contributions. Click for Introduction and tips and tricks in Crystallization, Derivatization, Diffraction, Symmetry, Structure Solution, Structure Refinement, and Structure Analysis.

 

Item 4: Topic Discussion

HKL2000 has a built-in feature (Reprocess) to reintegrate raw date (frames) with unit cell parameters fixed at the values obtained after postrefinement using Scalepack. Any comments, experience, or recommendations?

David Garboczi (NIAID): I used to do this with the script form of denzo.  I've read and thought that refining the cell during integration was a little suspect.  After all, if one can't trust that the cell dimensions are fixed enough to define your crystal, maybe that crystal isn't worth it.  Mosflm finds the cell dimensions first and then integrates.  I would definitely recommend reprocessing and would like to know about the other buttons in HKL2000 For instance, our absorption correction button clicks like it works, but the logfile says "Unknown keyword: absorption".
 
We are using XDS a lot as well and like its complete and current documentation. Its radiation damage correction algorithm has helped our anomalous signal, such that I doubt we would have solved several structures without it.
http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/

 

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

 


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