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Newsletter No. 309
March 2, 2015

ACA News, IUCr Newsletter, IUCr Meetings List

FEBRUARY 2015 PUBLICATIONS BY MEMBERS OF THE GROUP  


1: Acharya P, Lusvarghi S, Bewley CA, Kwong PD. HIV-1 gp120 as a therapeutic
target: navigating a moving labyrinth. Expert Opin Ther Targets. 2015 Feb
27:1-19. PubMed PMID: 25724219.

2: Deshmukh L, Ghirlando R,
Clore GM. Conformation and dynamics of the Gag
polyprotein of the human immunodeficiency virus 1 studied by NMR spectroscopy.
Proc Natl Acad Sci U S A. 2015 Feb 23. pii: 201501985. PubMed PMID: 25713345.

3: Anthis NJ,
Clore GM. Visualizing transient dark states by NMR spectroscopy. Q
Rev Biophys. 2015 Feb;48:35-116. PubMed PMID: 25710841.

4: Kim MS, Lapkouski M, Yang W, Gellert M. Crystal structure of the V(D)J
recombinase RAG1-RAG2. Nature. 2015 Feb 26;518:507-11. PubMed PMID: 25707801.

5: Gassman NR, Coskun E, Stefanick DF, Horton JK, Jaruga P, Dizdaroglu M, Wilson
SH
. Bisphenol a promotes cell survival following oxidative DNA damage in mouse
fibroblasts. PLoS One. 2015 Feb 18;10(2):e0118819. doi:
10.1371/journal.pone.0118819. eCollection 2015. PubMed PMID: 25693136.

6: Lountos GT, Cherry S, Tropea JE, Waugh DS. Structural analysis of human
dual-specificity phosphatase 22 complexed with a phosphotyrosine-like substrate.
Acta Crystallogr F Struct Biol Commun. 2015 Feb;71:199-205. PubMed PMID: 25664796.

7: Çağlayan M, Horton JK, Prasad R, Wilson SH. Complementation of aprataxin
deficiency by base excision repair enzymes. Nucleic Acids Res. 2015 Feb
27;43(4):2271-2281. PubMed PMID: 25662216.

8: Chen MC, Murat P, Abecassis K, Ferré-D'Amaré AR, Balasubramanian S. Insights
into the mechanism of a G-quadruplex-unwinding DEAH-box helicase. Nucleic Acids
Res. 2015 Feb 27;43(4):2223-2231. PubMed PMID: 25653156.

9: Edlefsen PT, Rolland M, Hertz T, Tovanabutra S, Gartland AJ, deCamp AC,
Magaret CA, Ahmed H, Gottardo R, Juraska M, McCoy C, Larsen BB, Sanders-Buell E,
Carrico C, Menis S, Bose M; RV144 Sequencing Team, Arroyo MA, O'Connell RJ,
Nitayaphan S, Pitisuttithum P, Kaewkungwal J, Rerks-Ngarm S, Robb ML, Kirys T,
Georgiev IS, Kwong PD, Scheffler K, Pond SL, Carlson JM, Michael NL, Schief WR,
Mullins JI, Kim JH, Gilbert PB. Comprehensive Sieve Analysis of Breakthrough
HIV-1 Sequences in the RV144 Vaccine Efficacy Trial. PLoS Comput Biol. 2015 Feb
3;11(2):e1003973. doi: 10.1371/journal.pcbi.1003973. eCollection 2015 Feb. PubMed
PMID: 25646817
.


For timely listing, please send a heads-up E-mail to the Editor upon publication.
TIPS AND TRICKS - The Cross-Linking Effect of PEG
(Click for PDF reader to view articles)


Michael Garavito: One of the unfortunate by-products of keeping PEG stock solutions in water is that they will form peroxides and aldehydes. They will slowly cross-link the surface of some crystals. However, it is dependent on the nature of your protein's composition of surface residues, so not every protein cyrstal does this.

I had one case where PEG4000 grown crystals would be resistant to dissolving and would easily bend; the thinner rods would spring back staight. After placing the crystals into buffer known to dissolve them, I poked the crystals hard and the insides squeezed out like toothpaste, leaving an empty sack behind. the bottom-line is that fresh crystals diffracted better than old crystals because of this cross-linking.

Suggestions: (1) Make your PEG stocks up fresh or store them in the freezer as aliquots; (2) Remove oxidized PEGs from your stocks (See Ray et al. Biochemistry, 30, 6866-6875, 1991 and Jurnak, J. Cryst. Growth, 76, 577-582, 1986); (3) Check to see if freshly grown crystals behave better.

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

TOPIC DISCUSSION - Data for Refinement and Deposition/Publication

Xinhua Ji (NCI): Concluding Remarks - During our discussion, I also consulted with the instructors and lecturers of the Cold Spring Harbor Laboratory 2014 course X-ray Method in Structural Biology. Taken together, the following are recommended: (1) A single date set should be used for structure solution, refinement, and deposition; (2) For the highest resolution (outmost) shell, the I/s(I) value should be  > 1.0 and the completeness should be > 50%; and (3) At the claimed resolution of the structure, the overall completeness should be > 93% and the completeness for the outmost shell should be > 70% as shown in the table below.

 

Scaled Data Set

At Claimed Resolution

Overall

Outmost Shell

Overall

Outmost Shell

Completeness (%)

 

> 50

> 93

> 70

I/s(I)

 

> 1.0

 

 

CC1/2

 

> 0.15*

 

 

*Value to be tested and optimized.

ARCHIVE: Test-set-and-R-free, Twinning, Low Resolution Crystallography, PHASER, HKL2000, Parallel Expression, Structural Genomics, NCS, Missing Atoms, Trends in CrystallographyAbsorption Correction, Data for Refinement and Publication.

LECTURES AND TUTORIALS NEW ADDITION - ACHESYM

RIGAKU WEBINAR SERIES (2009 - PRESENT)

LOW RESOLUTION PHASING AND REFINEMENT (2011)

CRYSTALLOGRAPHY: SEEING THINGS IN A DIFFERENT LIGHT (2013)

CRYSTALLOGRAPHY: FOR ASPIRING CRYSTALLOGRAPHERS (2013)

 STRUCTURE FACTOR TUTORIAL BY KEVIN COWTAN (2014)

DATA COLLECTION FOR STRUCTURE DETERMENATION (2014)

ACHESYM: AN ALGORITHM AND SERVER FOR STANDARDIZED PLACEMENT OF MACROMOLECULAR MODELS IN THE UNIT CELL (2014)

 LINKS NEW ADDITION -  ACHESYM     

Databases: BMCD, CryoD, DisProt, ExPASy, HAD, HIC-Up, Metal Sites, NDBPDB, PDBe
,
                 Protein Geometry Database, Scattering

Programs: CCP4, COOT, DSSR, HKLPHENIX, PyMOL, SOLVE, USF, XDS


Servers: ACHESYM,
Anisotropy, CheckMyMetal, Crystal, C6, Dali, DSSR, ESPript
              Grade, PDBePISA, PhyreProbity, Protein, Robetta Fragment & HHpred  

Facilities: 
APS SER-CAT, APS SAXS Capabilities

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