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Newsletter No. 413
January 20, 2020

ACA News, IUCr Newsletter, IUCr Meetings List

Understanding Biology through Structure, March 16-20, 2020

DECEMBER 2019 PUBLICATIONS BY MEMBERS OF THE GROUP  

1: Ruszkowski M, Sekula B, Ruszkowska A, Contestabile R, Nogues I, Angelaccio S, 
Szczepaniak A, Dauter Z. Structural basis of methotrexate and pemetrexed action
on serine hydroxymethyltransferases revealed using plant models
. Sci Rep. 2019
Dec 23;9(1):19614. doi: 10.1038/s41598-019-56043-4. PubMed PMID: 31873125; PubMed
Central PMCID: PMC6928210.

2: Natarajan K, Margulies DH. Cutting antigenic peptides down to size. J Biol
Chem. 2019 Dec 6;294(49):18545-18546. doi: 10.1074/jbc.H119.011803. PubMed PMID:
31811048.

3: Watts NR, Palmer IW, Eren E, Steven AC, Wingfield PT. Capsids of hepatitis B
virus e antigen with authentic C termini are stabilized by electrostatic
interactions
. FEBS Lett. 2019 Dec 2. doi: 10.1002/1873-3468.13706. [Epub ahead of
print] PubMed PMID: 31792961.

4: Aguilar OA, Sampaio IS, Rahim MMA, Samaniego JD, Tilahun ME, Krishnamoorthy M,
Popović B, Babić M, Krmpotić A, Treanor B,
Margulies DH, Allan DSJ, Makrigiannis
AP, Jonjić S, Carlyle JR. Mouse Cytomegalovirus m153 Protein Stabilizes
Expression of the Inhibitory NKR-P1B Ligand Clr-
b. J Virol. 2019 Dec 12;94(1).
pii: e01220-19. doi: 10.1128/JVI.01220-19. Print 2019 Dec 12. PubMed PMID:
31597762.

5: Suddala KC, Zhang J. High-affinity recognition of specific tRNAs by an mRNA
anticodon-binding groove
. Nat Struct Mol Biol. 2019 Dec;26(12):1114-1122. doi:
10.1038/s41594-019-0335-6. Epub 2019 Dec 2. PubMed PMID: 31792448.

6: Li S, Su Z, Lehmann J, Stamatopoulou V, Giarimoglou N, Henderson FE, Fan L,
Pintilie GD, Zhang K, Chen M, Ludtke SJ, Wang YX, Stathopoulos C, Chiu W, Zhang
J
. Structural basis of amino acid surveillance by higher-order tRNA-mRNA
interactions
. Nat Struct Mol Biol. 2019 Dec;26(12):1094-1105. doi:
10.1038/s41594-019-0326-7. Epub 2019 Nov 18. PubMed PMID: 31740854; PubMed
Central PMCID: PMC6899168.

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 - Recommandations?


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"


LOW RESOLUTION PHASING AND REFINEMENT (2011)

 Data Collection Strategies (2013)

 STRUCTURE FACTOR TUTORIAL (2014)

DATA COLLECTION FOR STRUCTURE DETERMENATION (2014)

CRYSTAL CLEAR (2014)

LITERATURE ON CRYSTALLOGRAPHY THEORY AND METHODS (2017)

PROTEIN CRYSTALLOGRAPHY Methods and Protocols (2017)

 Understanding Biology Through Structure (2017)

 On the state of crystallography at the dawn of the electron microscopy revolution (2017)

 The Fascinating World of Crystallography (2018)

 Data science skills for referees: I biological X-ray crystallography  (2018)

Correcting the public record of biological crystallography (2019)


 LINKS - Suggestions?

Databases: DisProt, ExPASy, HAD, HIC-Up, NDBPDB, PDBe
, Protein Geometry

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


Servers: ACHESYM,
Anisotropy, C6@C3, DaliESPript, Grade, PDBePISA, Phyre2,
             MolProbity, RestraintLib,

Copyright © NIH X-Ray Diffraction Group                       Maintained by Dr. Xinhua Ji
on the NIH-NCI-CCR-MCL server (https://mcl1.ncifcrf.gov)