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Newsletter No. 405
September 16, 2019

ACA News, IUCr Newsletter, IUCr Meetings List

Understanding Biology through Structure, March 16-20, 2020

AUGUST 2019 PUBLICATIONS BY MEMBERS OF THE GROUP  


1: Christenson ET, Isaac DT, Yoshida K, Lipo E, Kim JS, Ghirlando R, Isberg RR,
Banerjee A. The iron-regulated vacuolar Legionella pneumophila MavN protein is a
transition-metal transporter
. Proc Natl Acad Sci U S A. 2019 Aug 20. pii:
201902806. doi: 10.1073/pnas.1902806116. [Epub ahead of print] PubMed PMID:
31431530.

2: Ye Y, Xia D. A spiral path to unfolding. Nat Struct Mol Biol. 2019 Aug 19.
doi: 10.1038/s41594-019-0284-0. [Epub ahead of print] PubMed PMID: 31427794.

3: Solomon WC, Myint W, Hou S, Kanai T, Tripathi R, Kurt Yilmaz N, Schiffer CA,
Matsuo H. Mechanism for APOBEC3G catalytic exclusion of RNA and non-substrate
DNA
. Nucleic Acids Res. 2019 Aug 22;47(14):7676-7689. doi: 10.1093/nar/gkz550.
PubMed PMID: 31424549; PubMed Central PMCID: PMC6698744.

4: Trachman RJ, Ferré-D'Amaré AR. Tracking RNA with light: selection, structure,
and design of fluorescence turn-on RNA aptamers
. Q Rev Biophys. 2019 Aug
19;52:e8. doi: 10.1017/S0033583519000064. PubMed PMID: 31423956.

5: Lubkowski J, Wlodawer A. Geometric considerations support the
double-displacement catalytic mechanism of l-asparaginase
. Protein Sci. 2019 Aug
19. doi: 10.1002/pro.3709. [Epub ahead of print] PubMed PMID: 31423681.

6: Tugarinov V,
Clore GM. Exchange saturation transfer and associated NMR
techniques for studies of protein interactions involving high-molecular-weight
systems
. J Biomol NMR. 2019 Aug 12. doi: 10.1007/s10858-019-00244-6. [Epub ahead
of print] PubMed PMID: 31407202.

7: Chittori S, Hong J, Bai Y, Subramaniam S. Structure of the primed state of the
ATPase domain of chromatin remodeling factor ISWI bound to the nucleosome
.
Nucleic Acids Res. 2019 Aug 12. pii: gkz670. doi: 10.1093/nar/gkz670. [Epub ahead
of print] PubMed PMID: 31402386.

8: Trachman RJ 3rd, Stagno JR, Conrad C, Jones CP, Fischer P, Meents A, Wang YX,
Ferré-D'Amaré AR. Co-crystal structure of the iMango-III fluorescent RNA aptamer
using an X-ray free-electron laser
. Acta Crystallogr F Struct Biol Commun. 2019
Aug 1;75(Pt 8):547-551. doi: 10.1107/S2053230X19010136. Epub 2019 Aug 2. PubMed
PMID: 31397326; PubMed Central PMCID: PMC6688663.

9: Schmidt T, Schwieters CD,
Clore GM. Spatial domain organization in the HIV-1
reverse transcriptase p66 homodimer precursor probed by double electron-electron
resonance EPR
. Proc Natl Acad Sci U S A. 2019 Aug 5. pii: 201911086. doi:
10.1073/pnas.1911086116. [Epub ahead of print] PubMed PMID: 31383767.

10: Walters KJ. Ubiquitin in disguise unveils a cryptic binding site in 1.2-MDa
anaphase-promoting complex/cyclosome
. Proc Natl Acad Sci U S A. 2019 Aug
27;116(35):17142-17144. doi: 10.1073/pnas.1911388116. Epub 2019 Aug 1. PubMed
PMID: 31371495.


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 Mariusz Jaskólski

Mariusz Jaskólski
Workshop by IUCr Committee on Data, Vienna, August 18, 2019

 Understanding Biology Through Structure 2017

 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)