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Newsletter No. 407
October 21, 2019

ACA News, IUCr Newsletter, IUCr Meetings List

Understanding Biology through Structure, March 16-20, 2020

SEPTEMBER 2019 PUBLICATIONS BY MEMBERS OF THE GROUP  


1: Phillips BT, Williams JG, Atchley DT, Xu X, Li JL, Adams AL, Johnson KL, Hall
TMT
. Mass spectrometric identification of candidate RNA-binding proteins
associated with Transition Nuclear Protein mRNA in the mouse testis
. Sci Rep.
2019 Sep 20;9(1):13618. doi: 10.1038/s41598-019-50052-z. PubMed PMID: 31541158.

2: LaBranche CC, Henderson R, Hsu A, Behrens S, Chen X, Zhou T, Wiehe K, Saunders
KO, Alam SM, Bonsignori M, Borgnia MJ, Sattentau QJ, Eaton A, Greene K, Gao H,
Liao HX, Williams WB, Peacock J, Tang H, Perez LG, Edwards RJ, Kepler TB, Korber
BT, Kwong PD, Mascola JR, Acharya P, Haynes BF, Montefiori DC.
Neutralization-guided design of HIV-1 envelope trimers with high affinity for the
unmutated common ancestor of CH235 lineage CD4bs broadly neutralizing antibodies
.
PLoS Pathog. 2019 Sep 17;15(9):e1008026. doi: 10.1371/journal.ppat.1008026.
eCollection 2019 Sep. PubMed PMID: 31527908.

3: Dearborn AD, Marcotrigiano J. Hepatitis C Virus Structure: Defined by What It
Is Not
. Cold Spring Harb Perspect Med. 2019 Sep 9. pii: a036822. doi:
10.1101/cshperspect.a036822. [Epub ahead of print] PubMed PMID: 31501263.

4: Iwamoto N, Mason RD, Song K, Gorman J, Welles HC, Arthos J, Cicala C, Min S,
King HAD, Belli AJ, Reimann KA, Foulds KE,
Kwong PD, Lifson JD, Keele BF,
Roederer M. Blocking α(4)β(7) integrin binding to SIV does not improve virologic
control
. Science. 2019 Sep 6;365(6457):1033-1036. doi: 10.1126/science.aaw7765.
PubMed PMID: 31488690.

5: Sacks D, Bhiman JN, Wiehe K, Gorman J,
Kwong PD, Morris L, Moore PL. Somatic
hypermutation to counter a globally rare viral immunotype drove off-track
antibodies in the CAP256-VRC26 HIV-1 V2-directed bNAb lineage
. PLoS Pathog. 2019
Sep 3;15(9):e1008005. doi: 10.1371/journal.ppat.1008005. eCollection 2019 Sep.
PubMed PMID: 31479499; PubMed Central PMCID: PMC6743783.

6: Gibbs ME, Lountos GT, Gumpena R, Waugh DS. Crystal structure of UDP-glucose
pyrophosphorylase from Yersinia pestis, a potential therapeutic target against
plague
. Acta Crystallogr F Struct Biol Commun. 2019 Sep 1;75(Pt 9):608-615. doi:
10.1107/S2053230X19011154. PubMed PMID: 31475928; PubMed Central PMCID:
PMC6718147.

7: Chittori S, Hong J,
Bai Y, Subramaniam S. Structure of the primed state of the
ATPase domain of chromatin remodeling factor ISWI bound to the nucleosome
.
Nucleic Acids Res. 2019 Sep 26;47(17):9400-9409. doi: 10.1093/nar/gkz670. PubMed
PMID: 31402386; PubMed Central PMCID: PMC6755096.

8: Fernandez AJ, Daniel EJP, Mahajan SP, Gray JJ, Gerken TA, Tabak LA, Samara NL.
The structure of the colorectal cancer-associated enzyme GalNAc-T12 reveals how
nonconserved residues dictate its function
. Proc Natl Acad Sci U S A. 2019 Sep
23. pii: 201902211. doi: 10.1073/pnas.1902211116. [Epub ahead of print] PubMed
PMID: 31548401.

For timely listing, please send a heads-up E-mail to the Editor upon publication.
TIPS, TRICKS, METHODS - Contributions?

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

TOPIC DISCUSSIONSuggestions?

ARCHIVE: Test-set-and-R-free, Twinning, Low Resolution Crystallography, PHASER, HKL2000, Parallel Expression, NCS, Missing Atoms, Trends in CrystallographyAbsorption Correction, Data for Refinement and PublicationValidation, Table 1.

LECTURES AND TUTORIALS - Recommendations?


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)

 Data Collection Strategies (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)

A GLIMPSE OF STRUCTURAL BIOLOGY THROUGH X-RAY CRYSTALLOGRAPHY (2014)

CRYSTAL CLEAR (2014)

NATIVE SAD IS MATURING (2015)

LITERATURE ON CRYSTALLOGRAPHY THEORY AND METHODS (2017)

PROTEIN CRYSTALLOGRAPHY Methods and Protocols (2017)

 Understanding Biology Through Structure (2017)

 The Fascinating World of Crystallography (2018)

Correcting the public record of biological crystallography (2019)


 LINKS - Suggestions?

Databases: BMCDDisProt, ExPASy, HAD, HIC-Up, Metal Sites, NDBPDB, PDBe
,
                 Protein Geometry, Scattering

Programs: CCP4, COOT, DSSR, HKLPHENIX, PyMOL, SOLVE, XDS


Servers: ACHESYM,
Anisotropy, CheckMyMetal, Crystal, C6, Dali, DSSR, ESPript
              Grade, PDBePISA, Phyre, MolProbity, Protein, Robetta Fragment, HHpred,
 
            RestraintLib,


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 (https://mcl1.ncifcrf.gov)