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Newsletter No. 305
December 15, 2014

100 Years of X-ray Crystallography (IYCr2014)

Movie, Song, Movie, Lecture

ACA News, IUCr Newsletter, IUCr Meetings List

NOVEMBER 2014 PUBLICATIONS BY MEMBERS OF THE GROUP  

1: Bird GH, Irimia A, Ofek G, Kwong PD, Wilson IA, Walensky LD. Stapled HIV-1
peptides recapitulate antigenic structures and engage broadly neutralizing
antibodies. Nat Struct Mol Biol. 2014 Nov 24. doi: 10.1038/nsmb.2922.
PubMed PMID: 25420104.

2: Freudenthal BD, Beard WA, Perera L, Shock DD, Kim T, Schlick T, Wilson SH.
Uncovering the polymerase-induced cytotoxicity of an oxidized nucleotide. Nature.
2014 Nov 17. doi: 10.1038/nature13886. PubMed PMID: 25409153.

3: Meyerson JR, Rao P, Kumar J, Chittori S, Banerjee S, Pierson J, Mayer ML,
Subramaniam S. Self-assembled monolayers improve protein distribution on holey
carbon cryo-EM supports. Sci Rep. 2014 Nov 18;4:7084. doi: 10.1038/srep07084.
PubMed PMID: 25403871.

4: Beard WA, Shock DD, Batra VK, Prasad R, Wilson SH. Substrate-induced DNA
Polymerase β Activation. J Biol Chem. 2014 Nov 7;289(45):31411-22. doi:
10.1074/jbc.M114.607432. PubMed PMID: 25261471.

For timely listing, please send a heads-up E-mail to the Editor upon publication.
TIPS AND TRICKS - The Cross-Linking Effect of PEG


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
(Click for PDF reader to view articles)

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 - Structure Factor Tutorial

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)

 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)