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Newsletter No. 303
November 3, 2014

100 Years of X-ray Crystallography (IYCr2014)

Movie, Song, Movie, Lecture

ACA News, IUCr Newsletter, IUCr Meetings List

OCTOBER 2014 PUBLICATIONS BY MEMBERS OF THE GROUP  

1: Georgiev I, Joyce MG, Yang Y, Pancera M, Gorman J, Acharya P, Stewart-Jones G,
Druz A, Cheng C, Mascola JR,
Kwong PD. Uncleaved Soluble gp140 Constructs with
Retained Native-like Trimer Conformation and Antigenicity. AIDS Res Hum
Retroviruses. 2014 Oct;30(S1):A9. PubMed PMID: 25357972.

2: Soto CS, Ofek G, Joyce MG, Zhang B, McKee K, Mascola JR,
Kwong PD. Maturation
Pathways for the Broad and Potent Antibody 10E8 Using a Combination of Next
Generation Sequencing, Bioinformatics and Functional Analysis. AIDS Res Hum
Retroviruses. 2014 Oct;30(S1):A21. PubMed PMID: 25357587.

3: Pancera M, Druz A, Zhou T, O'Dell S, Louder M, Madani N, Herschhorn A,
Sodroski J, Mascola JR,
Kwong PD. Structure of BMS-806, a Small-molecule HIV-1
Entry Inhibitor, Bound to BG505 SOSIP.664 HIV-1 Env Trimer. AIDS Res Hum
Retroviruses. 2014 Oct;30(S1):A151. PubMed PMID: 25357424.

4: Kwon YD, Georgiev IS, Zhang B, McKee K, O'Dell S, Druz A, Shi W, Connors M,
Mascola JR,
Kwong PD. Enhancing the Solubility of HIV-1-neutralizing Antibody
10E8. AIDS Res Hum Retroviruses. 2014 Oct;30(S1):A150. PubMed PMID: 25357420.

5: Druz A, Pancera M, Acharya P, Zhou T, Joyce G, Ofek A,
Kwong PD. Transient
Protein Expression Facilitates X-ray Structural Studies of HIV-1. AIDS Res Hum
Retroviruses. 2014 Oct;30(S1):A148-A149. PubMed PMID: 25357414.

6: Acharya P, Zhou T, Soto C, Chen L, Luongo TS, Moquin S, Georgiev IS, Schmidt
SD, Louder MK, Joyce MG, Yang Y, Zhang B, Scheid J, Nussenzweig MC, Mascola JR,
Kwong PD. CD4-binding-Site Recognition by VH1-46 Germline-derived HIV-1
Neutralizers. AIDS Res Hum Retroviruses. 2014 Oct;30(S1):A120-A121. PubMed PMID:
25357335
.

7: Cheng C, Georgiev I, Joyce MG, Chen X, Bossert A, Kong WP,
Kwong PD, Mascola
JR. Optimization of a Clade A Env Outer Domain for Enhanced Binding to Germlines
of Diverse VRC01 Class Antibodies. AIDS Res Hum Retroviruses. 2014
Oct;30(S1):A117-A118. PubMed PMID: 25357324.

8: Chen L,
Kwong PD. "Canyon Shielding" of the CD4-Binding Site on HIV-1 Trimer.
AIDS Res Hum Retroviruses. 2014 Oct;30(S1):A117. PubMed PMID: 25357323.

9: Gorman J, Yang Y, Druz A, Baxa U,
Kwong PD. Structure-based Design of Trimeric
V1V2 Antigens. AIDS Res Hum Retroviruses. 2014 Oct;30(S1):A1-A7. PubMed PMID:
25357272
.

10: Shen HH, Leyton DL, Shiota T, Belousoff MJ, Noinaj N, Lu J, Holt SA, Tan K,
Selkrig J, Webb CT, Buchanan SK, Martin LL, Lithgow T. Reconstitution of a
nanomachine driving the assembly of proteins into bacterial outer membranes. Nat
Commun. 2014 Oct 24;5:5078. doi: 10.1038/ncomms6078. PubMed PMID: 25341963.

11: Munro JB, Gorman J, Ma X, Zhou Z, Arthos J, Burton DR, Koff WC, Courter JR,
Smith AB 3rd,
Kwong PD, Blanchard SC, Mothes W. Conformational dynamics of single
HIV-1 envelope trimers on the surface of native virions. Science. 2014 Oct 8.
pii: 1254426. [Epub ahead of print] PubMed PMID: 25298114.

12: Pancera M, Zhou T, Druz A, Georgiev IS, Soto C, Gorman J, Huang J, Acharya P,
Chuang GY, Ofek G, Stewart-Jones GB, Stuckey J, Bailer RT, Joyce MG, Louder MK,
Tumba N, Yang Y, Zhang B, Cohen MS, Haynes BF, Mascola JR, Morris L, Munro JB,
Blanchard SC, Mothes W, Connors M,
Kwong PD. Structure and immune recognition of
trimeric pre-fusion HIV-1 Env. Nature. 2014 Oct 23;514(7523):455-61. doi:
10.1038/nature13808. Epub 2014 Oct 8. PubMed PMID: 25296255.

13: Wlodawer A. On the prompt update of literature references in the Protein Data
Bank. Acta Crystallogr D Biol Crystallogr. 2014 Oct 1;70(Pt 10):2779. doi:
10.1107/S1399004714009973. Epub 2014 Sep 30. PubMed PMID: 25286862.

14: Brown HA, Roth G, Holzapfel G, Shen S, Rahbari K, Ireland J, Zou Z, Sun PD.
Development of an improved mammalian overexpression method for human CD62L.
Protein Expr Purif. 2014 Oct 5. pii: S1046-5928(14)00215-0. doi:
10.1016/j.pep.2014.09.018. [Epub ahead of print] PubMed PMID: 25286402.

15: Ryu KS, Tugarinov V, Clore GM. Probing the Rate-Limiting Step for
Intramolecular Transfer of a Transcription Factor between Specific Sites on the
Same DNA Molecule by (15)N(z)-Exchange NMR Spectroscopy. J Am Chem Soc. 2014 Oct
1. [Epub ahead of print] PubMed PMID: 25253516; PubMed Central PMCID: PMC4210153.

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 a resolution for structure deposition/publication can be done at the final stage of the refiment. A guide line I have been using 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 Academy 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.

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.

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)