logo2a.gif

Newsletter No. 311
April 20, 2015

ACA News, IUCr Newsletter, IUCr Meetings List

MARCH 2015 PUBLICATIONS BY MEMBERS OF THE GROUP  


1: Yu B, Swatkoski S, Holly A, Lee LC, Giroux V, Lee CS, Hsu D, Smith JL, Yuen G,
Yue J, Ann DK, Simpson RM, Creighton CJ, Figg WD, Gucek M, Luo J. Oncogenesis
driven by the Ras/Raf pathway requires the SUMO E2 ligase Ubc9. Proc Natl Acad
Sci U S A. 2015 Mar 24. pii: 201415569. PubMed PMID: 25805818.

2: Chuang GY, Zhang B, McKee K, O'Dell S, Kwon YD, Zhou T, Blinn J, Lloyd K,
Parks R, Von Holle T, Ko SY, Kong WP, Pegu A, Wang K, Baruah K, Crispin M,
Mascola JR, Moody MA, Haynes BF, Georgiev IS,
Kwong PD. Eliminating antibody
polyreactivity through addition of N-linked glycosylation. Protein Sci. 2015 Mar
19. doi: 10.1002/pro.2682. [Epub ahead of print] PubMed PMID: 25800131.

3: Noinaj N, Rollauer SE, Buchanan SK. The β-barrel membrane protein insertase
machinery from Gram-negative bacteria. Curr Opin Struct Biol. 2015 Mar
18;31:35-42. doi: 10.1016/j.sbi.2015.02.012. Review. PubMed PMID: 25796031.

4: Saunders KO, Pegu A, Georgiev IS, Zeng M, Joyce MG, Yang ZY, Ko SY, Chen X,
Schmidt SD, Haase AT, Todd JP, Bao S,
Kwong PD, Rao SS, Mascola JR, Nabel GJ.
Sustained delivery of a broadly neutralizing antibody in non-human primates
confers long-term protection against SHIV infection. J Virol. 2015 Mar 18. pii:
JVI.00210-15. [Epub ahead of print] PubMed PMID: 25787288.

5: Raran-Kurussi S, Keefe K,
Waugh DS. Positional effects of fusion partners on
the yield and solubility of MBP fusion proteins. Protein Expr Purif. 2015 Mar
14;110:159-164. doi: 10.1016/j.pep.2015.03.004. PubMed PMID: 25782741.

6: Jones CP, Ferré-D'Amaré AR. RNA quaternary structure and global symmetry.
Trends Biochem Sci. 2015 Apr;40(4):211-220. doi: 10.1016/j.tibs.2015.02.004. Epub
2015 Mar 13. Review. PubMed PMID: 25778613.

7: Lee YS, Gao Y,
Yang W. How a homolog of high-fidelity replicases conducts
mutagenic DNA synthesis. Nat Struct Mol Biol. 2015 Apr;22(4):298-303. doi:
10.1038/nsmb.2985. Epub 2015 Mar 16. PubMed PMID: 25775266.

8: Baber JL, Louis JM,
Clore GM. Dependence of Distance Distributions Derived
from Double Electron-Electron Resonance Pulsed EPR Spectroscopy on Pulse-Sequence
Time. Angew Chem Int Ed Engl. 2015 Mar 10. doi: 10.1002/anie.201500640. [Epub
ahead of print] .

9: Georgiev IS, Joyce MG, Yang Y, Sastry M, Zhang B, Baxa U, Chen RE, Druz A,
Lees CR, Narpala S, Schön A, Van Galen J, Chuang GY, Gorman J, Harned A, Pancera
M, Stewart-Jones GB, Cheng C, Freire E, McDermott AB, Mascola JR,
Kwong PD.
Single-chain soluble BG505.SOSIP gp140 trimers as structural and antigenic mimics
of mature closed HIV-1 Env. J Virol. 2015 Mar 4. pii: JVI.03451-14. [Epub ahead
of print] PubMed PMID: 25740988.

10: Ten Broeke T, van Spriel A, Sun P, Leusen J. Meeting report on
immunoreceptors 2014. FASEB J. 2015 Mar;29(3):740-4. doi: 10.1096/fj.15-0302ufm.
PubMed PMID: 25733692.

11: Thapar R. Structure-specific nucleic acid recognition by L-motifs and their
diverse roles in expression and regulation of the genome. Biochim Biophys Acta.
2015 Mar 4. pii: S1874-9399(15)00054-1. doi: 10.1016/j.bbagrm.2015.02.006. [Epub
ahead of print] Review. PubMed PMID: 25748361.

12: Gardner MR, Kattenhorn LM, Kondur HR, von Schaewen M, Dorfman T, Chiang JJ,
Haworth KG, Decker JM, Alpert MD, Bailey CC, Neale ES Jr, Fellinger CH, Joshi VR,
Fuchs SP, Martinez-Navio JM, Quinlan BD, Yao AY, Mouquet H, Gorman J, Zhang B,
Poignard P, Nussenzweig MC, Burton DR,
Kwong PD, Piatak M Jr, Lifson JD, Gao G,
Desrosiers RC, Evans DT, Hahn BH, Ploss A, Cannon PM, Seaman MS, Farzan M.
AAV-expressed eCD4-Ig provides durable protection from multiple SHIV challenges.
Nature. 2015 Mar 5;519(7541):87-91. doi: 10.1038/nature14264. Epub 2015 Feb 18.
PubMed PMID: 25707797.


For timely listing, please send a heads-up E-mail to the Editor upon publication.
TIPS AND TRICKS - Contributions?  (Click for PDF reader to view articles)


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) Date sets used for structure solution and refinement should be deposited as they are; (2) For the highest resolution (outmost) shell, the I/s(I) value should be  > 1.0 and the completeness should be > 50%; (3) At the claimed resolution of the structure, the overall completeness should be > 93% and the completeness for the outmost shell should be > 70%; and (4) Regardless of the claimed resolution, every reflection in the data set should be included for refinement and map calculations, and the entire data set (without truncation and sigma cutoff) should be deposited with the structure.

 

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 - ACHESYM

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)

ACHESYM: AN ALGORITHM AND SERVER FOR STANDARDIZED PLACEMENT OF MACROMOLECULAR MODELS IN THE UNIT CELL (2014)

 LINKS NEW ADDITION -  ACHESYM     

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: ACHESYM,
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)