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Newsletter No. 350
February 20, 2017

NIH's First Structures by XFEL Crystallography

ACA News, IUCr Newsletter, IUCr Meetings List

JANUARY 2017 PUBLICATIONS BY MEMBERS OF THE GROUP  


1: Kwong PD, Chuang GY, DeKosky BJ, Gindin T, Georgiev IS, Lemmin T, Schramm CA,
Sheng Z, Soto C, Yang AS, Mascola JR, Shapiro L. Antibodyomics: bioinformatics
technologies for understanding B-cell immunity to HIV-1
. Immunol Rev. 2017
Jan;275(1):108-128. doi: 10.1111/imr.12480. Review. PubMed PMID: 28133812.

2: Howard MJ, Rodriguez Y,
Wilson SH. DNA polymerase β uses its lyase domain in a
processive search for DNA damage
. Nucleic Acids Res. 2017 Jan 23. pii: gkx047.
doi: 10.1093/nar/gkx047. [Epub ahead of print] PubMed PMID: 28119421.

3: Ottaiano TF, Andrade SS, de Oliveira C, Silva MC, Buri MV, Juliano MA, Girão
MJ, Sampaio MU, Schmaier AH, Wlodawer A, Maffei FH, Oliva ML. Plasma Kallikrein
enhances platelet aggregation response by subthreshold doses of ADP
. Biochimie.
2017 Jan 20. pii: S0300-9084(16)30200-0. doi: 10.1016/j.biochi.2017.01.010. [Epub
ahead of print] PubMed PMID: 28115185.

4: Song H, Fang X, Jin L, Shaw GX, Wang YX, Ji X. The Functional Cycle of Rnt1p:
Five Consecutive Steps of Double-Stranded RNA Processing by a Eukaryotic RNase
III
. Structure. 2017 Jan 11. pii: S0969-2126(16)30403-8. doi:
10.1016/j.str.2016.12.013. [Epub ahead of print] PubMed PMID: 28111020.

5: Perera L, Freudenthal BD, Beard WA, Pedersen LG,
Wilson SH. Revealing the role
of the product metal in DNA polymerase β catalysis
. Nucleic Acids Res. 2017 Jan
20. pii: gkw1363. doi: 10.1093/nar/gkw1363. [Epub ahead of print] PubMed PMID:
28108654.

6: Wibmer CK, Gorman J, Ozorowski G, Bhiman JN, Sheward DJ, Elliott DH, Rouelle
J, Smira A, Joyce MG, Ndabambi N, Druz A, Asokan M, Burton DR, Connors M, Abdool
Karim SS, Mascola JR, Robinson JE, Ward AB, Williamson C,
Kwong PD, Morris L,
Moore PL. Structure and Recognition of a Novel HIV-1 gp120-gp41 Interface
Antibody that Caused MPER Exposure through Viral Escape
. PLoS Pathog. 2017 Jan
11;13(1):e1006074. doi: 10.1371/journal.ppat.1006074. PubMed PMID: 28076415;
PubMed Central PMCID: PMC5226681.

7: Çağlayan M, Horton JK, Dai DP, Stefanick DF,
Wilson SH. Oxidized nucleotide
insertion by pol β confounds ligation during base excision repair
. Nat Commun.
2017 Jan 9;8:14045. doi: 10.1038/ncomms14045. PubMed PMID: 28067232; PubMed
Central PMCID: PMC5228075.

8: Doria-Rose NA, Altae-Tran HR, Roark RS, Schmidt SD, Sutton MS, Louder MK,
Chuang GY, Bailer RT, Cortez V, Kong R, McKee K, O'Dell S, Wang F, Abdool Karim
SS, Binley JM, Connors M, Haynes BF, Martin MA, Montefiori DC, Morris L,
Overbaugh J,
Kwong PD, Mascola JR, Georgiev IS. Mapping Polyclonal HIV-1 Antibody
Responses via Next-Generation Neutralization Fingerprinting
. PLoS Pathog. 2017
Jan 4;13(1):e1006148. doi: 10.1371/journal.ppat.1006148. PubMed PMID: 28052137.


For timely listing, please send a heads-up E-mail to the Editor upon publication.
TIPS, TRICKS, METHODS - Microseeding Overcomes Hemihedral Twinning

Xinhua Ji
: It was recently reported that microseeding was used to produce untwinned crystals of an O-demethylase using twinned crystals as seeds (Acta Crystal. F72:897-902, 2016). Microseeding separates nucleation events from crystal growth events so that it can yield different crystal forms. Hence, it is promising that this technique can be used to produce untwinned crystals from twinned seeds.

Mariusz Jaskolski
: Stereochemical Restraint Libraries for Nucleic Acids

As part of a project aimed at revising the stereochemical restraint libraries for nucleic acids, a server, RestraintLib, has been created. It prepares external (custom) restraint files for the phosphate groups in DNA and RNA structures (submitted as PDB files). At present, the output is prepared for Refmac5, but other formats will be added as well.

The discussion of the new restraints and the method of their generation are presented in Nucleic Acids Research Advanced Access published August 12, 2016.


Zbigniew Dauter (NCI): Data Completeness from HKL2000 or HKL3000

Sometimes, relatively weak diffraction data processed with HKL2000 or HKL3000 show lower than expected completeness in the high resolution bins, in spite of otherwise high multiplicity and coverage of the reciprocal space. Apparently, this results from the automatic rejection of weak reflections, for which there are no good enough neighbors for building a “standard profile” within the vicinity defined by default value of the “Profile Fitting Radius”. To increase the high-resolution data completeness one can change the default profile fitting radius (in the “Index” window of HKL2000 or HKL3000) to much larger value, e.g. one third of the detector size. The number of “good” reflections, e.g. stronger than 5s(I), within the profile fitting radius can be visualized at the Xdisp window by clicking the “Prof Fit R” option.

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

TOPIC DISCUSSIONCrystal Structures

Mariusz Jaskolski: Pathological Behavior of Atomic Occupancy Factors
A number of PDB files have been detected and reported by Zbyszek Dauter, in which the atomic occupancy factors show a pathological behavior, where covalently connected atoms have uncorrelated fractional occupancies.  This pathology seems to have been spreading unnoticed because MR-generated structures inherited the pathology from some earlier models, and the refinement programs were not rigorous enough to block (or at least signal) the "infection".  You might be advised to check your PDB files for this pathology, using an ad-hoc server http://achesym.ibch.poznan.pl/occucheck/ by Marcin Kowiel.

ARCHIVE: Test-set-and-R-free, Twinning, Low Resolution Crystallography, PHASER, HKL2000, Parallel Expression, Structural Genomics, NCS, Missing Atoms, Trends in CrystallographyAbsorption Correction, Data for Refinement and Publication.

LECTURES AND TUTORIALS CRYSTALLOGRAPHY THEORY & METHODS



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)

NATIVE SAD IS MATURING (2015)

LITERATURE ON CRYSTALLOGRAPHY THEORY AND METHODS (2017)

 LINKS - New Server: RestraintLib
  

Databases: BMCD, CryoD, DisProt, ExPASy, HAD, HIC-Up, Metal Sites, NDBPDB, PDBe
,
                 Protein Geometry Database, Scattering

Programs: CCP4, COOT, DSSR, HKLPHENIX, PyMOL, SOLVE, USF, XDS


Servers: ACHESYM,
Anisotropy, CheckMyMetal, Crystal, C6, Dali, DSSR, ESPript
              Grade, PDBePISA, PhyreProbity, 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)