logo2a.gif

Newsletter No. 327
January 4, 2016

ACA News, IUCr Newsletter, IUCr Meetings List

DECEMBER 2015 PUBLICATIONS BY MEMBERS OF THE GROUP  

1: Cheng C, Pancera M, Bossert A, Schmidt SD, Chen R, Chen X, Druz A, Narpala S, 
Doria-Rose NA, McDermott AB, Kwong PD, Mascola JR. Immunogenicity of a Prefusion
HIV-1-Envelope Trimer in Complex with a Quaternary-Specific Antibody
. J Virol.
2015 Dec 30. pii: JVI.02380-15. [Epub ahead of print] PubMed PMID: 26719262.

2: Kiliszek A, Banaszak K,
Dauter Z, Rypniewski W. The first crystal structures
of RNA-PNA duplexes and a PNA-PNA duplex containing mismatches-toward anti-sense
therapy against TREDs
. Nucleic Acids Res. 2015 Dec 29. pii: gkv1513. [Epub ahead
of print] PubMed PMID: 26717983.

3: Pletneva NV, Pletnev VZ, Sarkisyan KS, Gorbachev DA, Egorov ES, Mishin AS,
Lukyanov KA,
Dauter Z, Pletnev S. Crystal Structure of Phototoxic Orange
Fluorescent Proteins with a Tryptophan-Based Chromophore
. PLoS One. 2015 Dec
23;10(12):e0145740. doi: 10.1371/journal.pone.0145740. eCollection 2015. PubMed
PMID: 26699366; PubMed Central PMCID: PMC4689385.

4: Gorman J, Soto C, Yang MM, Davenport TM, Guttman M, Bailer RT, Chambers M,
Chuang GY, DeKosky BJ, Doria-Rose NA, Druz A, Ernandes MJ, Georgiev IS,
Jarosinski MC, Joyce MG, Lemmin TM, Leung S, Louder MK, McDaniel JR, Narpala S,
Pancera M, Stuckey J, Wu X, Yang Y, Zhang B, Zhou T, Program NC, Mullikin JC,
Baxa U, Georgiou G, McDermott AB, Bonsignori M, Haynes BF, Moore PL, Morris L,
Lee KK, Shapiro L, Mascola JR, Kwong PD. Structures of HIV-1 Env V1V2 with
broadly neutralizing antibodies reveal commonalities that enable vaccine design
.
Nat Struct Mol Biol. 2015 Dec 21. doi: 10.1038/nsmb.3144. [Epub ahead of print]
PubMed PMID: 26689967.

5: Waugh DS. Crystal structures of MBP fusion proteins. Protein Sci. 2015 Dec 19.
doi: 10.1002/pro.2863. [Epub ahead of print] Review. PubMed PMID: 26682969.

6: Baird NJ, Inglese J, Ferré-D'Amaré AR. Rapid RNA-ligand interaction analysis
through high-information content conformational and stability landscapes
. Nat
Commun. 2015 Dec 7;6:8898. doi: 10.1038/ncomms9898. PubMed PMID: 26638992.

7: Nunes NN, Ferreira RS, Silva-Lucca RA, de Sá LF, de Oliveira AE, Correia MT,
Paiva PM,
Wlodawer A, Oliva ML. Potential of the Lectin/Inhibitor Isolated from
Crataeva tapia Bark (CrataBL) for Controlling Callosobruchus maculatus Larva
Development
. J Agric Food Chem. 2015 Dec 9;63(48):10431-6. doi:
10.1021/acs.jafc.5b03634. Epub 2015 Dec 1. PubMed PMID: 26568149.

For timely listing, please send a heads-up E-mail to the Editor upon publication.
TIPS AND TRICKS High-Resolution cryo-electron microscopy (cryoEM)

Cryo-electron microscopy (cryoEM) is an ensemble of techniques allowing the observation of biological specimens in their native environment at cryogenic temperatures in EM. For a recent cryoEM structure at high resolution, please see 2.2 Å resolution cryo-EM structure of b-galactosidase in complex with a cell-permeant inhibitor. For an overview, please see CryoEM at IUCrJ: a new era.

Small-angle X-ray scattering (SAXS) is capable of delivering structural information of biological macromolecules and their complexes in solution, small or large. For a recent example, the SAXS model for a ~500-kDa RapA:RNA polymerase complex (~230 angstroms in its longest dimension), please see Allosteric Activation of Bacterial Swi2/Snf2 Protein RapA by RNA Polymerase: Biochemical and Structural Studies.

ARCHIVE: Introduction, Pre-crystallization, Crystallization, Post-crystallization, Derivatization, Cryoprotection, Diffraction, Symmetry, Structure Solution, Structure Refinement, Structure Analysis & Presentation.

TOPIC DISCUSSION - Suggestions?

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 - Dr. Dauter's Lectures Are Back!

DR. ZBIGNIEW DAUTER'S LECTURES AT THE NIH (2005)
 

Part 1: "How to read international tables?"

Part 2: "Data collection strategy" and "Twinning"

           "Phasing methods - a general introduction to all methods"

Part 3: "SAD phasing, Quick halide soaking, and Radiation damage 

            with possible use of it for phasing"


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 (2014)

DATA COLLECTION FOR STRUCTURE DETERMENATION (2014)

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

NATIVE SAD IS MATURING (2015)

 LINKS - Suggestions?     

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)