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Newsletter No. 438
March 1, 2021

ACA News, IUCr Newsletter, IUCr Meetings List


FEBUARY 2021 PUBLICATIONS BY MEMBERS OF THE GROUP


1: Cai M, Huang Y, Lloyd J, Craigie R, Clore GM. A simple and cost-effective
protocol for high-yield expression of deuterated and selectively
isoleucine/leucine/valine methyl protonated proteins in Escherichia coli grown
in shaker flasks
. J Biomol NMR. 2021 Feb 4. doi: 10.1007/s10858-021-00357-x.
Epub ahead of print. PMID: 33538948.

2: Puig M, Ananthula S, Venna R, Kumar Polumuri S, Mattson E, Walker LM, Cardone
M, Takahashi M, Su S, Boyd LF, Natarajan K, Abdoulaeva G, Wu WW, Roderiquez G,
Hildebrand WH, Beaucage SL, Li Z, Margulies DH, Norcross MA. Alterations in the
HLA-B*57:01 Immunopeptidome by Flucloxacillin and Immunogenicity of Drug-
Haptenated Peptides
. Front Immunol. 2021 Feb 9;11:629399. doi:
10.3389/fimmu.2020.629399. PMID: 33633747; PMCID: PMC7900192.

3: Kuster A, Mozaffari NL, Wilkinson OJ, Wojtaszek JL, Zurfluh C, Przetocka S,
Zyla D, von Aesch C, Dillingham MS,
Williams RS, Sartori AA. A stapled peptide
mimetic of the CtIP tetramerization motif interferes with double-strand break
repair and replication fork protection
. Sci Adv. 2021 Feb 19;7(8):eabc6381. doi:
10.1126/sciadv.abc6381. PMID: 33608267.

4: Wilt HM, Yu P, Tan K, Wang YX, Stagno JR. Tying the knot in the
tetrahydrofolate (THF) riboswitch: A molecular basis for gene regulation
. J
Struct Biol. 2021 Feb 9;213(1):107703. doi: 10.1016/j.jsb.2021.107703. Epub
ahead of print. PMID: 33571639.

For timely listing, please send a heads-up E-mail to the Editor upon publication.
METHODS - Evolving data standards for cryo-EM structures

The development of cryo-EM is directly reflected by the growth of cryo-EM strructure depositions contributed worldwide to public data archived. The archiving systems and underlying data standards supporting depostioin, annotation, release, and validation of cyro-EM stuctures and the associated metadata describing cryo-EM experiments have been developed over time to support this growth. Recently,  CL Lawson, HM Berman, and W Chiu outlined the history of these systems and described the process by which data standards had been developed. For details, please click the link.

Reliable cryo-EM resolution estimation
A modified Fourier shell correlation (FSC) moehodology is introduced by Pawel Penczek, which is aimed addressing two fundamental problems that mar the use of FSC: the strong influence of mask-induced artifacts on resolution estimation and the lack of assessment of FSC uncertaninties stemming from the inability to determine the asscociated number of degrees of freedom. For details, please click the link.

New approach for  structure determination from tiny crystals
Many crystals can't be grown into crystals large enough for their atomic arrangements to be deciphered. To tackle this challenge, scientists at the U.S. DOE's Brookhaven National Laboratory and colleagues at Columbia University have developed a new approach for solving protein structure from tiny crystal. For details, please click the link.

ARCHIVE: Introduction, Pre-crystallization, Crystallization, Post-crystallization, Derivatization, Cryoprotection, Diffraction, Symmetry, Structure Solution, Structure Refinement, Structure Analysis & Presentation, Biophysical Methods, Sample Preparation.

DISCUSSIONSWhat do you as a structural biologist think of the use of AI by DeepMind to predict protein folds?

Please find an analysis by Prof. John Helliwell and share your thoughts with the community.

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.

READINGS AND TUTORIALS - Jennifer Doudna, Nobel Lecture 2020


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)

A Little Dictionary of Crystallography (2019)

Early history of cryo-cooling for macromolecular crystallography (2019)

Methods Comparison: XFEL vs microED (2020)

The data universe of structural biology (2020)

MicroED Methodology & Development (2020)

How to Speak, Lecture by Patrick Winston (2020)


 LINKS - PDB SARS-CoV-2 Resources (Link)

Databases: DisProt, ExPASy, HAD, HIC-Up, NDBPDB, PDBe
, Protein Geometry
                  SARS-CoV-2 Related Structures, PDB SARS-CoV-2 Resources,


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)