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Newsletter No. 416
March 2, 2020

ACA News, IUCr Newsletter, IUCr Meetings List

Understanding Biology through Structure, March 16-20, 2020

FEBRUARY 2020 PUBLICATIONS BY MEMBERS OF THE GROUP  

1: Ou L, Kong WP, Chuang GY, Ghosh M, Gulla K, O'Dell S, Varriale J, Barefoot N, 
Changela A, Chao CW, Cheng C, Druz A, Kong R, McKee K, Rawi R, Sarfo EK, Schön A,
Shaddeau A, Tsybovsky Y, Verardi R, Wang S, Wanninger TG, Xu K, Yang GJ, Zhang B,
Zhang Y, Zhou T; VRC Production Program, Arnold FJ, Doria-Rose NA, Lei QP, Ryan
ET, Vann WF, Mascola JR, Kwong PD. Preclinical Development of a Fusion Peptide
Conjugate as an HIV Vaccine Immunogen
. Sci Rep. 2020 Feb 20;10(1):3032. doi:
10.1038/s41598-020-59711-y. PubMed PMID: 32080235.

2: Sekula B, Ruszkowski M,
Dauter Z. S-adenosylmethionine synthases in plants:
Structural characterization of type I and II isoenzymes from Arabidopsis thaliana
and Medicago truncatula
. Int J Biol Macromol. 2020 Feb 11. pii:
S0141-8130(20)30238-5. doi: 10.1016/j.ijbiomac.2020.02.100. [Epub ahead of print]
PubMed PMID: 32057875.

3: Liu X, Liang B, Liu X, Amaro-Carambot E, Surman S,
Kwong PD, Graham BS,
Collins PL, Munir S. Human parainfluenza virus type 3 expressing the respiratory
syncytial virus pre-fusion F protein modified for virion packaging yields
protective intranasal vaccine candidates
. PLoS One. 2020 Feb 11;15(2):e0228572.
doi: 10.1371/journal.pone.0228572. eCollection 2020. PubMed PMID: 32045432;
PubMed Central PMCID: PMC7012412.

4: Tang WK, Borgnia MJ, Hsu AL, Esser L, Fox T, de Val N, Xia D. Structures of
AAA protein translocase Bcs1 suggest translocation mechanism of a folded protein
.
Nat Struct Mol Biol. 2020 Feb;27(2):202-209. doi: 10.1038/s41594-020-0373-0. Epub
2020 Feb 10. PubMed PMID: 32042153.

5: Boyoglu-Barnum S, Hutchinson GB, Boyington JC, Moin SM, Gillespie RA,
Tsybovsky Y, Stephens T, Vaile JR, Lederhofer J, Corbett KS, Fisher BE, Yassine
HM, Andrews SF, Crank MC, McDermott AB, Mascola JR, Graham BS, Kanekiyo M. Glycan
repositioning of influenza hemagglutinin stem facilitates the elicitation of
protective cross-group antibody responses
. Nat Commun. 2020 Feb 7;11(1):791. doi:
10.1038/s41467-020-14579-4. PubMed PMID: 32034141; PubMed Central PMCID:
PMC7005838.

6: Batra VK, Alnajjar KS, Sweasy JB, McKenna CE, Goodman MF,
Wilson SH. Revealing
an Internal Stabilization Deficiency in the DNA Polymerase β K289M Cancer Variant
through the Combined Use of Chemical Biology and X-ray Crystallography
.
Biochemistry. 2020 Feb 12. doi: 10.1021/acs.biochem.9b01072. [Epub ahead of
print] PubMed PMID: 31999437.


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 - Dictionary of Crystallography


A Little Dictionary of Crystallography (2019)

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)