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Newsletter No. 306
January 5, 2015
Happy New Year!

ACA News, IUCr Newsletter, IUCr Meetings List

DECEMBER 2014 PUBLICATIONS BY MEMBERS OF THE GROUP  

1: Kong L, Wilson IA, Kwong PD. Crystal structure of a fully glycosylated HIV-1
gp120 core reveals a stabilizing role for the glycan at Asn262. Proteins. 2014
Dec 26. doi: 10.1002/prot.24747. [Epub ahead of print] PubMed PMID: 25546301.

2: Horton JK, Gassman NR, Dunigan BB, Stefanick DF,
Wilson SH. DNA polymerase
β-dependent cell survival independent of XRCC1 expression. DNA Repair (Amst).
2014 Dec 3. pii: S1568-7864(14)00283-3. doi: 10.1016/j.dnarep.2014.11.008. [Epub
ahead of print] PubMed PMID: 25541391.

3: Fong Y, Datta S, Georgiev IS,
Kwong PD, Tomaras GD. Kernel-based logistic
regression model for protein sequence without vectorialization. Biostatistics.
2014 Dec 22. pii: kxu056. [Epub ahead of print] PubMed PMID: 25532524.

4: Acharya P, Luongo TS, Georgiev IS, Matz J, Schmidt SD, Louder MK, Kessler P,
Yang Y, McKee K, O'Dell S, Chen L, Baty D, Chames P, Martin L, Mascola JR, Kwong
PD
. Correction for Acharya et al., Heavy Chain-Only IgG2b Llama Antibody Effects
Near-Pan HIV-1 Neutralization by Recognizing a CD4-Induced Epitope That Includes
Elements of Coreceptor- and CD4-Binding Sites. J Virol. 2015 Jan 1;89(1):883-5.
doi: 10.1128/JVI.02621-14. Epub 2014 Dec 16. PubMed PMID: 25516606.

5: Qiu C, McCann KL, Wine RN, Baserga SJ, Hall TM. A divergent Pumilio repeat
protein family for pre-rRNA processing and mRNA localization. Proc Natl Acad Sci
U S A. 2014 Dec 30;111(52):18554-9. doi: 10.1073/pnas.1407634112. Epub 2014 Dec
15. PubMed PMID: 25512524.

6: Kowiel M, Jaskolski M, Dauter Z. ACHESYM: an algorithm and server for
standardized placement of macromolecular models in the unit cell. Acta
Crystallogr D Biol Crystallogr. 2014 Dec 1;70(Pt 12):3290-8. doi:
10.1107/S1399004714024572. Epub 2014 Nov 28. PubMed PMID: 25478846.

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 - Data Collection Strategies

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)


 LINKS NEW ADDITION - Protein Geometry Database      

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: 
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)