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Newsletter No. 379
June 18, 2018

ACA News, IUCr Newsletter, IUCr Meetings List

ACA 2018, FEBS 2018, Protein Society 2018

MAY 2018 PUBLICATIONS BY MEMBERS OF THE GROUP  


1: Lane KD, Mu J, Lu J, Windle ST, Liu A, Sun PD, Wellems TE. Selection of
Plasmodium falciparum cytochrome B mutants by putative PfNDH2 inhibitors
. Proc
Natl Acad Sci U S A. 2018 May 29. pii: 201804492. doi: 10.1073/pnas.1804492115.
[Epub ahead of print] PubMed PMID: 29844160.

2: Noble AJ, Dandey VP, Wei H, Brasch J, Chase J, Acharya P, Tan YZ, Zhang Z, Kim
LY, Scapin G, Rapp M, Eng ET, Rice WJ, Cheng A, Negro CJ, Shapiro L,
Kwong PD,
Jeruzalmi D, des Georges A, Potter CS, Carragher B. Routine single particle
CryoEM sample and grid characterization by tomography
. Elife. 2018 May 29;7. pii:
e34257. doi: 10.7554/eLife.34257. [Epub ahead of print] PubMed PMID: 29809143.

3: Bachas ST, Ferré-D'Amaré AR. Convergent Use of Heptacoordination for Cation
Selectivity by RNA and Protein Metalloregulators
. Cell Chem Biol. 2018 May 4.
pii: S2451-9456(18)30146-6. doi: 10.1016/j.chembiol.2018.04.016. [Epub ahead of
print] PubMed PMID: 29805037.

4: Cardone M, Garcia K, Tilahun ME, Boyd LF, Gebreyohannes S, Yano M, Roderiquez
G, Akue AD, Juengst L, Mattson E, Ananthula S, Natarajan K, Puig M, Margulies DH,
Norcross MA. A transgenic mouse model for HLA-B*57:01-linked abacavir drug
tolerance and reactivity
. J Clin Invest. 2018 May 21. pii: 99321. doi:
10.1172/JCI99321. [Epub ahead of print] PubMed PMID: 29782330.

5:
Kwong PD, Mascola JR. HIV-1 Vaccines Based on Antibody Identification, B Cell
Ontogeny, and Epitope Structure
. Immunity. 2018 May 15;48(5):855-871. doi:
10.1016/j.immuni.2018.04.029. Review. PubMed PMID: 29768174.

6: Trachman RJ 3rd, Abdolahzadeh A, Andreoni A, Cojocaru R, Knutson JR,
Ryckelynck M, Unrau PJ,
Ferré-D'Amaré AR. Crystal Structures of the Mango-II RNA
Aptamer Reveal Heterogeneous Fluorophore Binding and Guide Engineering of
Variants with Improved Selectivity and Brightness
. Biochemistry. 2018 May 24.
doi: 10.1021/acs.biochem.8b00399. [Epub ahead of print] PubMed PMID: 29768001.

7: Ceccon A, Schmidt T, Tugarinov V, Kotler SA, Schwieters CD, Clore GM.
Interaction of Huntingtin Exon-1 Peptides with Lipid-Based Micellar Nanoparticles
Probed by Solution NMR and Q-Band Pulsed EPR
. J Am Chem Soc. 2018 May
23;140(20):6199-6202. doi: 10.1021/jacs.8b02619. Epub 2018 May 14. PubMed PMID:
29727175.

8: Debnath S, Kosek D, Tagad HD, Durell SR, Appella DH, Acevedo R, Grishaev A,
Dyda F, Appella E, Mazur SJ. A trapped human PPM1A-phosphopeptide complex reveals
structural features critical for regulation of PPM protein phosphatase activity
.
J Biol Chem. 2018 May 25;293(21):7993-8008. doi: 10.1074/jbc.RA117.001213. Epub
2018 Mar 30. PubMed PMID: 29602904; PubMed Central PMCID: PMC5971455.

For timely listing, please send a heads-up E-mail to the Editor upon publication.
TIPS, TRICKS, METHODS A new MR-SAD algorithm

Recently, a  new MR-SAD algorithm was  reported  by Pavol Skubak, Navray Pannu, and co-workers in the IUCrJ (5:166-171, 2018), for automatic building of protein models from low-resolution X-ray diffraction data and a poor starting model. According to the authors, their algorithm uses a multivariate function to simultatnerously exploit informatino from both the initial partial model and low-resolution SAD data. Details of the algorithm and its application to six challenging structure determinations can be seen here.

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

TOPIC DISCUSSIONTable 1

A perspective article "Against Method: Table 1--Cui Bono?" was  recently published in Structure by Bernhard Rupp, pointing out that "Information contained in 'Table 1' is insufficient to evaluate or repeat the experiment, is redundant with information extractable from deposited diffraction data, and includes data items whose meaning is under increased scruitiny in the crystallographic community," and suggesting that "Direct and consistent extraction and analysis of data quality metrics from prefereably unmerged intensity data with graphical presentation of reciprocal space features, including impact on map and model features, should replace 'Table 1'."

Do you agree with Bernhard? Please share your opionion and ideas with fellow crystallographers.

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.

LECTURES AND TUTORIALS 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 (http://mcl1.ncifcrf.gov)