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Newsletter No. 302
October 20, 2014

100 Years of X-ray Crystallography (IYCr2014)

Movie, Song, Movie, Lecture

ACA News, IUCr Newsletter, IUCr Meetings List

SEPTEMBER 2014 PUBLICATIONS BY MEMBERS OF THE GROUP  


1: Jones CP, Ferré-D'Amaré AR. Crystal structure of a c-di-AMP riboswitch reveals
an internally pseudo-dimeric RNA. EMBO J. 2014 Sep 30. pii: e201489209. [Epub
ahead of print] PubMed PMID: 25271255.

2: Blaszczyk J, Lu Z, Li Y, Yan H, Ji X. Crystallographic and molecular dynamics
simulation analysis of Escherichia coli dihydroneopterin aldolase. Cell Biosci.
2014 Sep 2;4(1):52. doi: 10.1186/2045-3701-4-52. eCollection 2014. PubMed PMID:
25264482
; PubMed Central PMCID: PMC4176595.

3: Ingale J, Tran K, Kong L, Dey B, McKee K, Schief W,
Kwong PD, Mascola JR,
Wyatt RT. Hyperglycosylated stable core immunogens designed to present the CD4
binding site preferentially recognized by broadly neutralizing antibodies. J
Virol. 2014 Sep 24. pii: JVI.02614-14. PubMed PMID: 25253346.

4: Bouvin-Pley M, Morgand M, Meyer L, Goujard C, Moreau A, Mouquet H, Nussenzweig
M, Pace C, Ho D, Bjorkman PJ, Baty D, Chames P, Pancera M,
Kwong PD, Poignard P,
Barin F, Braibant M. Drift of the HIV-1 envelope glycoprotein gp120 toward
increased neutralization resistance over the course of the epidemic: a
comprehensive study using the most potent and broadly neutralizing monoclonal
antibodies. J Virol. 2014 Sep 17. pii: JVI.02083-14. PubMed PMID: 25231299.

5: Kepler TB, Liao HX, Alam SM, Bhaskarabhatla R, Zhang R, Yandava C, Stewart S,
Anasti K, Kelsoe G, Parks R, Lloyd KE, Stolarchuk C, Pritchett J, Solomon E,
Friberg E, Morris L, Karim SS, Cohen MS, Walter E, Moody MA, Wu X, Altae-Tran HR,
Georgiev IS,
Kwong PD, Boyd SD, Fire AZ, Mascola JR, Haynes BF. Immunoglobulin
Gene Insertions and Deletions in the Affinity Maturation of HIV-1 Broadly
Reactive Neutralizing Antibodies. Cell Host Microbe. 2014 Sep 10;16(3):304-13.
doi: 10.1016/j.chom.2014.08.006. PubMed PMID: 25211073; PubMed Central PMCID:
PMC4163498.

6: Huang J, Kang BH, Pancera M, Lee JH, Tong T, Feng Y, Georgiev IS, Chuang GY,
Druz A, Doria-Rose NA, Laub L, Sliepen K, van Gils MJ, de la Peña AT, Derking R,
Klasse PJ, Migueles SA, Bailer RT, Alam M, Pugach P, Haynes BF, Wyatt RT, Sanders
RW, Binley JM, Ward AB, Mascola JR,
Kwong PD, Connors M. Broad and potent HIV-1
neutralization by a human antibody that binds the gp41-gp120 interface. Nature.
2014 Sep 3. doi: 10.1038/nature13601. PubMed PMID: 25186731.

7: Zhang J, Ferré-D'Amaré AR. Dramatic Improvement of Crystals of Large RNAs by
Cation Replacement and Dehydration. Structure. 2014 Sep 2;22(9):1363-71. doi:
10.1016/j.str.2014.07.011. PubMed PMID: 25185828; PubMed Central PMCID:
PMC4177851.

8: Shaw GX, Li Y, Shi G, Wu Y, Cherry S, Needle D, Zhang D, Tropea JE, Waugh DS,
Yan H, Ji X. Structural enzymology and inhibition of the bi-functional folate
pathway enzyme HPPK-DHPS from the biowarfare agent Francisella tularensis. FEBS
J. 2014 Sep;281(18):4123-37. doi: 10.1111/febs.12896. PubMed PMID: 24975935.

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): High-resolution data, even not complete, always helps improve electron density that reveals additional structure features. Therefore, it is beneficial to include more data in the refinement. Claiming resolution for structure deposition/publication can be done at the final stage of the refiment. A guide line I have been using in my lab is shown below. Please comment and/or advise.

 

Refinement

Publication

Overall

Last Shell

Overall

Last Shell

Completeness (%)

> 85

> 50

> 93

> 70

I / s(I)

> 10

> 1

> 10

> 2

R-merge

< 0.10

< 0.50

< 0.10

< 0.50

 

scalepack

Scalepack.log*

output.sca

 

phenix.refine

(During refinement)

01_data.mtz

Containing all data from output.sca

phenix.refine

(Final refinement)

02_020.pdb*

02_020.log*

02_020_f_model.mtz*

 

Containing data at the claimed resolution

* Files for PDB deposition.

Mark Mayer (NICHD)I understand the benefit of using weak and incomplete data in high resolution shells for calculating maps and improving model building, especially with the routine use of rpim, cc and cc* at the stage of scaling supporting use of reflections in shells with with I/sigma < 2, but I don't understand how to proceed to the deposition/publication stage. After completing model building and refinement using all the data, why would we drop weak and incomplete data in the last round of refinement  to achieve  > 70% completeness and I/sigma > 2 or some other arbitrary cut off that will satisfy reviewers/PDB annotaters? If maps improve with weak and incomplete data in high resolution shells, then there is useful structural information, so why throw it away?

Mariusz Jaskolski (Polish Acadamy of Sciences)Thanks very much for initiating a discussion about the use of high-resolution reflections for refinement and at other stages of structure determination/publication.  I have a lot of comments and practical remarks in this area, and I have summarized some of them in a one-page document.

A number of similar questions are discussed in my chapter in one of the recent Erice books: M.Jaskolski (2013), High resolution macromolecular crystallography. In: Advancing Methods for Biomolecular Crystallography. R.Read, A.G.Urzhumtsev, V.Y.Lunin eds. Springer, 259-275.

Recommended Reading: Inclusion of weak high-resolution X-ray data for improvement of a group II intron structure.


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

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)