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Newsletter No. 402
July 15, 2019

ACA News, IUCr Newsletter, IUCr Meetings List

ACA 2019, FEBS 2019, Protein Society 2019

JUNE 2019 PUBLICATIONS BY MEMBERS OF THE GROUP  


1: Hood IV, Gordon JM, Bou-Nader C, Henderson FE, Bahmanjah S, Zhang J. Crystal
structure of an adenovirus virus-associated RNA
. Nat Commun. 2019 Jun
28;10(1):2871. doi: 10.1038/s41467-019-10752-6. PubMed PMID: 31253805.

2: Rotanova TV, Andrianova AG, Kudzhaev AM, Li M, Botos I, Wlodawer A, Gustchina
A
. New insights into structural and functional relationships between LonA
proteases and ClpB chaperones
. FEBS Open Bio. 2019 Jun 25. doi:
10.1002/2211-5463.12691. [Epub ahead of print] PubMed PMID: 31237118.

3: Beard WA, Horton JK, Prasad R, Wilson SH. Eukaryotic Base Excision Repair: New
Approaches Shine Light on Mechanism
. Annu Rev Biochem. 2019 Jun 20;88:137-162.
doi: 10.1146/annurev-biochem-013118-111315. PubMed PMID: 31220977.

4: Lindesmith LC, McDaniel JR, Changela A, Verardi R, Kerr SA, Costantini V,
Brewer-Jensen PD, Mallory ML, Voss WN, Boutz DR, Blazeck JJ, Ippolito GC, Vinje
J, Kwong PD, Georgiou G, Baric RS. Sera Antibody Repertoire Analyses Reveal
Mechanisms of Broad and Pandemic Strain Neutralizing Responses after Human
Norovirus Vaccination
. Immunity. 2019 Jun 18;50(6):1530-1541.e8. doi:
10.1016/j.immuni.2019.05.007. PubMed PMID: 31216462.

5: Lountos GT, Zhao XZ, Kiselev E, Tropea JE, Needle D, Pommier Y, Burke TR,
Waugh DS. Identification of a ligand binding hot spot and structural motifs
replicating aspects of tyrosyl-DNA phosphodiesterase I (TDP1) phosphoryl
recognition by crystallographic fragment cocktail screening
. Nucleic Acids Res.
2019 Jun 14. pii: gkz515. doi: 10.1093/nar/gkz515. [Epub ahead of print] PubMed
PMID: 31199869.

6: Greger IH, Mayer ML. Structural biology of glutamate receptor ion channels:
towards an understanding of mechanism
. Curr Opin Struct Biol. 2019 Jun
7;57:185-195. doi: 10.1016/j.sbi.2019.05.004. [Epub ahead of print] Review.
PubMed PMID: 31185364.

For timely listing, please send a heads-up E-mail to the Editor upon publication.
TIPS, TRICKS, METHODS - Date Collection with ID22 and Eiger16M

Fred Dyda (NIDDK): Last week we collected ID data at 50 ms / 0.2 degrees at 30% transmission. With these, 180 degree of data took only 45 s.
      This suggests that one could go faster with wider frames and/or higher transmission.
      John says that the limit in exposure time is 20 ms. This is where the stream server stars to choke in spitting out the .cbf files from the stream.

Fred Dyda (NIDDK): During a survey of data collection practices, it became apparent that most users do not take advantage of the current capabilities of ID22 and the Eiger16M. In particular it has been shown that excellent data can collected using 0.2 or 0.25 degrees / 0.05 sec speed so 200 degrees can be collected in 36 or 50 sec. One would of course have to increase transmission, but this should be possible as most people seem to collect at 80 or 90% attenuation. This should be OK, as all indicate that decay is dependent of totla accumulated does and is independent of dose rate.

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 - Data Collection Strategies

 The Fascinating World of 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 (https://mcl1.ncifcrf.gov)