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Newsletter No. 403
August 5, 2019

ACA News, IUCr Newsletter, IUCr Meetings List


JULY 2019 PUBLICATIONS BY MEMBERS OF THE GROUP  


1: Yang W, Seidman MM, Rupp WD, Gao Y. Replisome structure suggests mechanism for
continuous fork progression and post-replication repair
. DNA Repair (Amst). 2019
Jul 8:102658. doi: 10.1016/j.dnarep.2019.102658. [Epub ahead of print] Review.
PubMed PMID: 31303546.

2: Song H, Ji X. The mechanism of RNA duplex recognition and unwinding by
DEAD-box helicase DDX3X
. Nat Commun. 2019 Jul 12;10(1):3085. doi:
10.1038/s41467-019-11083-2. PubMed PMID: 31300642; PubMed Central PMCID:
PMC6626043.

3: Qiu C, Dutcher RC, Porter DF, Arava Y, Wickens M, Hall TMT. Distinct
RNA-binding modules in a single PUF protein cooperate to determine RNA
specificity
. Nucleic Acids Res. 2019 Jul 11. pii: gkz583. doi:
10.1093/nar/gkz583. [Epub ahead of print] PubMed PMID: 31294800.

4: Chao FA, Li Y, Zhang Y, Byrd RA. Probing the Broad Time Scale and
Heterogeneous Conformational Dynamics in the Catalytic Core of the Arf-GAP ASAP1
via Methyl Adiabatic Relaxation Dispersion
. J Am Chem Soc. 2019 Jul
31;141(30):11881-11891. doi: 10.1021/jacs.9b02602. Epub 2019 Jul 22. PubMed PMID:
31293161.

5: Dai DP, Prasad R, Strauss PR,
Wilson SH. The Pol β variant containing exon α
is deficient in DNA polymerase but has full dRP lyase activity
. Sci Rep. 2019 Jul
9;9(1):9928. doi: 10.1038/s41598-019-45846-0. PubMed PMID: 31289286; PubMed
Central PMCID: PMC6616571.

6: Gordon J, Pillon MC, Stanley RE. Nol9 Is a Spatial Regulator for the Human
ITS2 Pre-rRNA Endonuclease-Kinase Complex
. J Mol Biol. 2019 Jul 6. pii:
S0022-2836(19)30430-9. doi: 10.1016/j.jmb.2019.07.007. [Epub ahead of print]
PubMed PMID: 31288032.


7: Pillon MC, Lo YH, Stanley RE. IT'S 2 for the price of 1: Multifaceted ITS2
processing machines in RNA and DNA maintenance
. DNA Repair (Amst). 2019 Jul
8:102653. doi: 10.1016/j.dnarep.2019.102653. [Epub ahead of print] Review. PubMed
PMID: 31324529.

8: Bax A, Clore GM. Protein NMR: Boundless opportunities. J Magn Reson. 2019 Jul
9. pii: S1090-7807(19)30150-8. doi: 10.1016/j.jmr.2019.07.037. [Epub ahead of
print] PubMed PMID: 31311710.

9: Kong R, Duan H, Sheng Z, Xu K, Acharya P, Chen X, Cheng C, Dingens AS, Gorman
J, Sastry M, Shen CH, Zhang B, Zhou T, Chuang GY, Chao CW, Gu Y, Jafari AJ,
Louder MK, O'Dell S, Rowshan AP, Viox EG, Wang Y, Choi CW, Corcoran MM, Corrigan
AR, Dandey VP, Eng ET, Geng H, Foulds KE, Guo Y, Kwon YD, Lin B, Liu K, Mason RD,
Nason MC, Ohr TY, Ou L, Rawi R, Sarfo EK, Schön A, Todd JP, Wang S, Wei H, Wu W;
NISC Comparative Sequencing Program, Mullikin JC, Bailer RT, Doria-Rose NA,
Karlsson Hedestam GB, Scorpio DG, Overbaugh J, Bloom JD, Carragher B, Potter CS,
Shapiro L,
Kwong PD, Mascola JR. Antibody Lineages with Vaccine-Induced
Antigen-Binding Hotspots Develop Broad HIV Neutralization
. Cell. 2019 Jul
25;178(3):567-584.e19. doi: 10.1016/j.cell.2019.06.030. PubMed PMID: 31348886.



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): Last week we collected ID data at 50 ms / 0.2 degrees at 30% transmission. With these, 180 degree of data took only 45 s.
      This suggests that one could go faster with wider frames and/or higher transmission.
      John says that the limit in exposure time is 20 ms. This is where the stream server stars to choke in spitting out the .cbf files from the stream.

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.

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 - 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)