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Newsletter No. 395
April 1, 2019

ACA News, IUCr Newsletter, IUCr Meetings List

ACA 2019, FEBS 2019, Protein Society 2019

MARCH 2019 PUBLICATIONS BY MEMBERS OF THE GROUP  

1: Jin L, Song H, Tropea JE, Needle D, Waugh DS, Gu S, Ji X. The molecular
mechanism of dsRNA processing by a bacterial Dicer
. Nucleic Acids Res. 2019 Mar
27. pii: gkz208. doi: 10.1093/nar/gkz208. [Epub ahead of print] PubMed PMID:
30916338.

2: Sana G, Madigan JP, Gartner JJ, Fourrez M, Lin J, Qutob N, Narayan J, Shukla
S, Ambudkar SV, Xia D, Rosenberg SA, Gottesman MM, Samuels Y, Gillet JP. Exome
sequencing of ABCB5 identifies recurrent melanoma mutations that result in
increased proliferative and invasive capacities
. J Invest Dermatol. 2019 Mar 21.
pii: S0022-202X(19)31330-2. doi: 10.1016/j.jid.2019.01.036. [Epub ahead of print]
PubMed PMID: 30905807.

3: Krebs SJ, Kwon YD, Schramm CA, Law WH, Donofrio G, Zhou KH, Gift S, Dussupt V,
Georgiev IS, Schätzle S, McDaniel JR, Lai YT, Sastry M, Zhang B, Jarosinski MC,
Ransier A, Chenine AL, Asokan M, Bailer RT, Bose M, Cagigi A, Cale EM, Chuang GY,
Darko S, Driscoll JI, Druz A, Gorman J, Laboune F, Louder MK, McKee K, Mendez L,
Moody MA, O'Sullivan AM, Owen C, Peng D, Rawi R, Sanders-Buell E, Shen CH,
Shiakolas AR, Stephens T, Tsybovsky Y, Tucker C, Verardi R, Wang K, Zhou J, Zhou
T, Georgiou G, Alam SM, Haynes BF, Rolland M, Matyas GR, Polonis VR, McDermott
AB, Douek DC, Shapiro L, Tovanabutra S, Michael NL, Mascola JR, Robb ML,
Kwong
PD
,
, Doria-Rose NA. Longitudinal Analysis Reveals Early Development of Three
MPER-Directed Neutralizing Antibody Lineages from an HIV-1-Infected Individual
.
Immunity. 2019 Mar 19;50(3):677-691.e13. doi: 10.1016/j.immuni.2019.02.008. Epub
2019 Mar 12. PubMed PMID: 30876875.

4: Kim TS, Zhang L, Il Ahn J, Meng L, Chen Y, Lee E, Bang JK, Lim JM, Ghirlando
R, Fan L, Wang YX, Kim BY, Park JE, Lee KS. Molecular architecture of a
cylindrical self-assembly at human centrosomes
. Nat Commun. 2019 Mar
11;10(1):1151. doi: 10.1038/s41467-019-08838-2. PubMed PMID: 30858376; PubMed
Central PMCID: PMC6411776.

5: Oertell K, Florián J, Haratipour P, Crans DC, Kashemirov BA, Wilson SH,
McKenna CE, Goodman MF. A Transition-State Perspective on Y-Family DNA Polymerase
η Fidelity in Comparison with X-Family DNA Polymerases λ and β
. Biochemistry.
2019 Mar 14. doi: 10.1021/acs.biochem.9b00087. [Epub ahead of print] PubMed PMID:
30839203.

6: Niessen KA, Xu M, George DK, Chen MC, Ferré-D'Amaré AR, Snell EH, Cody V, Pace
J, Schmidt M, Markelz AG. Protein and RNA dynamical fingerprinting. Nat Commun.
2019 Mar 4;10(1):1026. doi: 10.1038/s41467-019-08926-3. PubMed PMID: 30833555;
PubMed Central PMCID: PMC6399446.

7: Lu J, Van Laethem F, Bhattacharya A, Craveiro M, Saba I, Chu J, Love NC,
Tikhonova A, Radaev S, Sun X, Ko A, Arnon T, Shifrut E, Friedman N, Weng NP,
Singer A, Sun PD. Molecular constraints on CDR3 for thymic selection of
MHC-restricted TCRs from a random pre-selection repertoire
. Nat Commun. 2019 Mar
4;10(1):1019. doi: 10.1038/s41467-019-08906-7. PubMed PMID: 30833553; PubMed
Central PMCID: PMC6399321.

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): 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.


Detergent-Free Membrane Protein System |  In a newly published paper in PNAS, a team led by Dr. Youzhong Guo of VCU's School of Pharmacy used a new detergent-free method that allowed them to examine the membrane of an Escherichia coli cell, with lipids still in place, providing the clearest view ever of cell membrane that yields unexpected structure. 

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

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)