logo2a.gif

Newsletter No. 304
December 1, 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
(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): Click and see my recent lab seminar at the Macromolecular Crystallography Laboratory (MCL) of the NCI for further discussion. Please let me know if you would like to discuss on this topic.

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

RCAKU 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)