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Newsletter No. 410
December 2, 2019


Portrait of a Crystallographer

ACA News, IUCr Newsletter, IUCr Meetings List

Understanding Biology through Structure, March 16-20, 2020

NOVEMBER 2019 PUBLICATIONS BY MEMBERS OF THE GROUP  

1: Cai M, Huang Y, Shen Y, Li M, Mizuuchi M, Ghirlando R, Mizuuchi K, Clore GM.
Probing transient excited states of the bacterial cell division regulator MinE by
relaxation dispersion NMR spectroscopy
. Proc Natl Acad Sci U S A. 2019 Nov 26.
pii: 201915948. doi: 10.1073/pnas.1915948116. [Epub ahead of print] PubMed PMID:
31772021.

2: Garrett DS, Cai M,
Clore GM. XIPP: multi-dimensional NMR analysis software. J
Biomol NMR
. 2019 Nov 20. doi: 10.1007/s10858-019-00286-w. [Epub ahead of print]
PubMed PMID: 31748843.

3: Shizu R, Yokobori K, Perera L, Pedersen L, Negishi M. Ligand induced
dissociation of the AR homodimer precedes AR monomer translocation to the
nucleus
. Sci Rep. 2019 Nov 13;9(1):16734. doi: 10.1038/s41598-019-53139-9. PubMed
PMID: 31723170; PubMed Central PMCID: PMC6853983.

4: Prattes M, Lo YH, Bergler H, Stanley RE. Shaping the Nascent Ribosome:
AAA-ATPases in Eukaryotic Ribosome Biogenesis
. Biomolecules. 2019 Nov 7;9(11).
pii: E715. doi: 10.3390/biom9110715. Review. PubMed PMID: 31703473.

5: Cai M, Huang Y, Craigie R,
Clore GM. A simple protocol for expression of
isotope-labeled proteins in Escherichia coli grown in shaker flasks at high cell
density
. J Biomol NMR. 2019 Dec;73(12):743-748. doi: 10.1007/s10858-019-00285-x.
Epub 2019 Nov 1. PubMed PMID: 31677040.

6: Roy NS, Jian X, Soubias O, Zhai P, Hall JR, Dagher JN, Coussens NP, Jenkins
LM, Luo R, Akpan IO, Hall MD, Byrd RA, Yohe ME, Randazzo PA. Interaction of the N
terminus of ADP-ribosylation factor with the PH domain of the GTPase-activating
protein ASAP1 requires phosphatidylinositol 4,5-bisphosphate
. J Biol Chem. 2019
Nov 15;294(46):17354-17370. doi: 10.1074/jbc.RA119.009269. Epub 2019 Oct 6.
PubMed PMID: 31591270; PubMed Central PMCID: PMC6873180.

7: Ye Y, Xia D. Author Correction: AAA ATPASES: A spiral path to unfolding. Nat
Struct Mol Biol. 2019 Nov;26(11):1078. doi: 10.1038/s41594-019-0317-8. PubMed
PMID: 31542791.

8: 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 Nov 4;47(19):10134-10150. doi: 10.1093/nar/gkz515. PubMed PMID: 31199869;
PubMed Central PMCID: PMC6821334.

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 - Crystallography and electron microscopy



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)

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