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Newsletter No. 250
 December 5, 2011
 

ACA News, IUCr Meetings List

NOVEMBER 2011 PUBLICATIONS BY MEMBERS OF THE GROUP  


1: McLellan JS, Pancera M, Carrico C, Gorman J, Julien JP, Khayat R, Louder R,
Pejchal R, Sastry M, Dai K, O'Dell S, Patel N, Shahzad-Ul-Hussan S, Yang Y, Zhang
B, Zhou T, Zhu J, Boyington JC, Chuang GY, Diwanji D, Georgiev I, Do Kwon Y, Lee 
D, Louder MK, Moquin S, Schmidt SD, Yang ZY, Bonsignori M, Crump JA, Kapiga SH,
Sam NE, Haynes BF, Burton DR, Koff WC, Walker LM, Phogat S, Wyatt R, Orwenyo J,
Wang LX, Arthos J, Bewley CA, Mascola JR, Nabel GJ, Schief WR, Ward AB, Wilson
IA, Kwong PD. Structure of HIV-1 gp120 V1/V2 domain with broadly neutralizing
antibody PG9. Nature. 2011 Nov 23. doi: 10.1038/nature10696. [Epub ahead of
print] PubMed PMID: 22113616.

2: Barnard TJ, Gumbart J, Peterson JH, Noinaj N, Easley NC, Dautin N, Kuszak AJ, 
Tajkhorshid E, Bernstein HD, Buchanan SK. Molecular Basis for the Activation of a
Catalytic Asparagine Residue in a Self-Cleaving Bacterial Autotransporter. J Mol 
Biol. 2011 Nov 7. [Epub ahead of print] PubMed PMID: 22094314.

3: Yamashita S, Lukacik P, Barnard TJ, Noinaj N, Felek S, Tsang TM, Krukonis ES, 
Hinnebusch BJ, Buchanan SK. Structural Insights into Ail-Mediated Adhesion in
Yersinia pestis. Structure. 2011 Nov 9;19(11):1672-82. PubMed PMID: 22078566.

4: Anthis NJ, Doucleff M, Clore GM. Transient, sparsely populated compact States 
of apo and calcium-loaded calmodulin probed by paramagnetic relaxation
enhancement: interplay of conformational selection and induced fit. J Am Chem
Soc. 2011 Nov 23;133(46):18966-74. PubMed PMID: 21999431.

5: Yang W. Surviving the sun: repair and bypass of DNA UV lesions. Protein Sci.
2011 Nov;20(11):1781-9. doi: 10.1002/pro.723. PubMed PMID: 21898645.

For timely listing, please send a heads-up E-mail to the Editor upon publication.
TIPS AND TRICKS - Small Molecule Crystal Data Collection

Bernard D Santarsiero: You can collect 5-10deg images, and go ahead and collect 360deg. I usually use 1-3 seconds exposures, depending on the diffraction.  The detector is set as close as possible, to get data to 0.8-0.9A resolution. For a MAR CCD 300mm detector, that's around 90-100mm, with the wavelength set at 0.8A, or around 15.5KeV in energy. You can process it with HKL2000 or XDS easily.


Zbigniew Dauter: I completely agree with Bernard, but I have one additional comment. The range of intensities from small molecule crystals is usually much higher than from protein crystals. It is therefore practically always necessary to collect them in multiple (sometimes even three) passes with different effective exposure time (or beam attenuation) and resolution range. Unfortunately people often forget about it and as a result very many  strongest reflections are overloaded and lost.

ARCHIVE: Introduction, Pre-crystallization, Crystallization, Post-crystallization, Derivatization, Cryoprotection, Diffraction, Symmetry, Structure Solution, Structure Refinement, Structure Analysis & Presentation.

TOPIC DISCUSSION - Suggested Topic?

ARCHIVE: Test-set-and-R-free, Twinning, Low Resolution Crystallography, PHASER, HKL2000, Parallel Expression, Structural Genomics, NCS, Missing Atoms, Trends in Crystallography,  Absorption Correction.
DR. ZBIGNIEW DAUTER'S LECTURE 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"
 LINKS - New Addition: CheckMyMetal

Databases: BMCD, CryoD, DisProt, ExPASy, HAD, HIC-Up, Metal Sites, NDB, PDB, PDBe,
                  Scattering
Programs: CCP4, COOT, HKL, PHENIX, PyMOL, SOLVE, USF, XDS
Servers: CheckMyMetal, Crystal, C6, Dali, ESPript, Phyre, Probity, Protein
 
Copyright © NIH X-Ray Diffraction Group                       Maintained by Dr. Xinhua Ji
on the NIH-NCI-CCR-MCL server (http://mcl1.ncifcrf.gov)