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Newsletter No. 384
October 1, 2018

ACA News, IUCr Newsletter, IUCr Meetings List

ACA 2019, FEBS 2019, Protein Society 2019

SEPTEMBER 2018 PUBLICATIONS BY MEMBERS OF THE GROUP  


1: Hickman AB, Voth AR, Ewis H, Li X, Craig NL, Dyda F. Structural insights into
the mechanism of double strand break formation by Hermes, a hAT family eukaryotic
DNA transposase
. Nucleic Acids Res. 2018 Sep 20. doi: 10.1093/nar/gky838. [Epub
ahead of print] PubMed PMID: 30239795.

2:
Wlodawer A, Dauter Z. Do structures matter any more? FEBS J. 2018
Sep;285(18):3322-3323. doi: 10.1111/febs.14630. PubMed PMID: 30221844.

3: Dauter Z,
Wlodawer A. Crystallographically correct but confusing presentation
of structural models deposited in the Protein Data Bank
. Acta Crystallogr D
Struct Biol. 2018 Sep 1;74(Pt 9):939-945. doi: 10.1107/S2059798318009828. Epub
2018 Sep 5. PubMed PMID: 30198902; PubMed Central PMCID: PMC6130463.

4: Gumpena R, Lountos GT, Waugh DS. MBP-binding DARPins facilitate the
crystallization of an MBP fusion protein
. Acta Crystallogr F Struct Biol Commun.
2018 Sep 1;74(Pt 9):549-557. doi: 10.1107/S2053230X18009901. Epub 2018 Aug 29.
PubMed PMID: 30198887; PubMed Central PMCID: PMC6130421.

5: Ceccon A, Clore GM, Tugarinov V. Decorrelating Kinetic and Relaxation
Parameters in Exchange Saturation Transfer NMR: A Case Study of N-Terminal
Huntingtin Peptides Binding to Unilamellar Lipid Vesicles
. J Phys Chem B. 2018
Sep 12. doi: 10.1021/acs.jpcb.8b07112. [Epub ahead of print] PubMed PMID:
30156416.

6: Kardava L, Sohn H, Youn C, Austin JW, Wang W, Buckner CM, Justement JS, Melson
VA, Roth GE, Hand MA, Gittens KR, Kwan RW, Sneller MC, Li Y, Chun TW, Sun PD,
Pierce SK, Moir S. IgG3 regulates tissue-like memory B cells in HIV-infected
individuals
. Nat Immunol. 2018 Sep;19(9):1001-1012. doi:
10.1038/s41590-018-0180-5. Epub 2018 Aug 13. PubMed PMID: 30104633.

7: Dearborn AD, Eren E, Watts NR, Palmer IW, Kaufman JD, Steven AC, Wingfield PT.
Structure of an RNA Aptamer that Can Inhibit HIV-1 by Blocking Rev-Cognate RNA
(RRE) Binding and Rev-Rev Association
. Structure. 2018 Sep 4;26(9):1187-1195.e4.
doi: 10.1016/j.str.2018.06.001. Epub 2018 Jul 12. PubMed PMID: 30017564.

8: Zhou BR, Jiang J, Ghirlando R, Norouzi D, Sathish Yadav KN, Feng H, Wang R,
Zhang P, Zhurkin V, Bai Y. Revisit of Reconstituted 30-nm Nucleosome Arrays
Reveals an Ensemble of Dynamic Structures
. J Mol Biol. 2018 Sep 14;430(18 Pt
B):3093-3110. doi: 10.1016/j.jmb.2018.06.020. Epub 2018 Jun 27. PubMed PMID:
29959925.


For timely listing, please send a heads-up E-mail to the Editor upon publication.
TIPS, TRICKS, METHODS FSEARCH: cryo-EM Map Replacement

FSEARCH: cryo-EM Map Replacement |  Recently, a  hybrid method that integrates X-ray crystallography with cryo-EM for structure determination is presented by Lingxiao Zeng, Wei Ding, and Quan Hao in the IUCrJ (5:382-389, 2018). The starting point is a cryo-EM map  and the end point is a high-resolution crystal structure. The workflow of the method and four case study examples can be seen here.

A new MR-SAD algorithm | 
Recently, a  new MR-SAD algorithm was  reported  by Pavol Skubak, Navray Pannu, and co-workers in the IUCrJ (5:166-171, 2018), for automatic building of protein models from low-resolution X-ray diffraction data and a poor starting model. According to the authors, their algorithm uses a multivariate function to simultatnerously exploit informatino from both the initial partial model and low-resolution SAD data. Details of the algorithm and its application to six challenging structure determinations can be seen here.

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

TOPIC DISCUSSIONTable 1

A perspective article "Against Method: Table 1--Cui Bono?" was  recently published in Structure by Bernhard Rupp, pointing out that "Information contained in 'Table 1' is insufficient to evaluate or repeat the experiment, is redundant with information extractable from deposited diffraction data, and includes data items whose meaning is under increased scruitiny in the crystallographic community," and suggesting that "Direct and consistent extraction and analysis of data quality metrics from prefereably unmerged intensity data with graphical presentation of reciprocal space features, including impact on map and model features, should replace 'Table 1'."

Do you agree with Bernhard? Please share your opionion and ideas with fellow crystallographers.

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.

LECTURES AND TUTORIALS CRYSTALLOGRAPHY


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)

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)

 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 (http://mcl1.ncifcrf.gov)