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Newsletter No. 204
 September 21, 2009

Biophysical Society 54th Annual Meeting (02/20-24/2010)

AUGUST 2009 PUBLICATIONS BY MEMBERS OF THE GROUP  

1: Brzuszkiewicz A, Nowak E, Dauter Z, Dauter M, Cieśliński H, Długołecka A, Kur 
J. Structure of EstA esterase from psychrotrophic Pseudoalteromonas sp. 643A
covalently inhibited by monoethylphosphonate. Acta Crystallogr Sect F Struct Biol
Cryst Commun. 2009 Sep 1;65(Pt 9):862-5. PubMed PMID: 19724118.

2: Carrozza MJ, Stefanick DF, Horton JK, Kedar PS, Wilson SH. PARP inhibition
during alkylation-induced genotoxic stress signals a cell cycle checkpoint
response mediated by ATM. DNA Repair (Amst). 2009 Aug 28. PubMed PMID: 19717351.

3: Tu C, Zhou X, Tropea JE, Austin BP, Waugh DS, Court DL, Ji X. Structure of ERA
in complex with the 3' end of 16S rRNA: Implications for ribosome biogenesis.
Proc Natl Acad Sci U S A. 2009 Aug 17. PubMed PMID: 19706445.

4: Gustchina E, Louis JM, Frisch C, Ylera F, Lechner A, Bewley CA, Clore GM.
Affinity maturation by targeted diversification of the CDR-H2 loop of a
monoclonal Fab derived from a synthetic naïve human antibody library and directed
against the internal trimeric coiled-coil of gp41 yields a set of Fabs with
improved HIV-1 neutralization potency and breadth. Virology. 2009 Aug 18.
PubMed PMID: 19695655.

5: Wu X, Zhou T, O'Dell S, Wyatt RT, Kwong PD, Mascola JR. Mechanism of HIV-1
Resistance to Monoclonal Antibody b12 that Effectively Targets the Site of CD4
Attachment. J Virol. 2009 Aug 19. PubMed PMID: 19692465.

6: Nowak E, Brzuszkiewicz A, Dauter M, Dauter Z, Rosenbaum G. To scavenge or not 
to scavenge: that is the question. Acta Crystallogr D Biol Crystallogr. 2009
Sep;65(Pt 9):1004-6. Epub 2009 Aug 14. PubMed PMID: 19690379.

7: Pletnev S, Morozova KS, Verkhusha VV, Dauter Z. Rotational order-disorder
structure of fluorescent protein FP480. Acta Crystallogr D Biol Crystallogr. 2009
Sep;65(Pt 9):906-12. Epub 2009 Aug 6. PubMed PMID: 19690368.

8: Im YJ, Wollert T, Boura E, Hurley JH. Structure and function of the
ESCRT-II-III interface in multivesicular body biogenesis. Dev Cell. 2009
Aug;17(2):234-43. PubMed PMID: 19686684.

9: Dorjsuren D, Wilson DM 3rd, Beard WA, McDonald JP, Austin CP, Woodgate R,
Wilson SH, Simeonov A. A real-time fluorescence method for enzymatic
characterization of specialized human DNA polymerases. Nucleic Acids Res. 2009
Aug 14. PubMed PMID: 19684079.
TIPS AND TRICKS

(4) Crystal Screen Optimization Server

It is a GUI written by P Hubbard to calculate 2D gradients for crystal screen optimization (much like a web 2.0 version of Hampton’s “Make Tray” utility). It gives a handy print out of recipes and records for people who make their optimization trays by hand.

(3) Cryoprotectant Database

(2) CCP4 wiki on Crystallization of Protein-DNA Complexes

(1) Hampton Research Crystal Screens 1 & 2 as Additives

Annie Hassell and co-workers at Glaxo Smithkline have had lots of success using the Hampton Research Crystal Screens (HRCS) 1 & 2 as additives. Sometimes these improve the crystal quality whereas the 96 Additive Screen does not. What they have not had a great deal of success with is determining which component of the added reagent is responsible for improving the crystal quality. Does not appear that it is just one component in many cases.

They generally use 5% of the sparse matrix screen added to the well. When they get a hit, they further optimize the concentration of the reagent to add to the well.

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

TOPIC DISCUSSION - Suggested Topics?

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"
Copyright © NIH X-Ray Diffraction Group                       Maintained by Dr. Xinhua Ji
on the NIH-NCI-CCR-MCL server (http://mcl1.ncifcrf.gov)