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Newsletter No. 358
July 31, 2017

ACA News, IUCr Newsletter, IUCr Meetings List

JULY 2017 PUBLICATIONS BY MEMBERS OF THE GROUP  

1: Hwang JK, Wang C, Du Z, Meyers RM, Kepler TB, Neuberg D, Kwong PD, Mascola JR,
Joyce MG, Bonsignori M, Haynes BF, Yeap LS, Alt FW. Sequence intrinsic somatic
mutation mechanisms contribute to affinity maturation of VRC01-class HIV-1
broadly neutralizing antibodies
. Proc Natl Acad Sci U S A. 2017 Jul 26. pii:
201709203. doi: 10.1073/pnas.1709203114. PubMed PMID: 28747530.

2: Trachman RJ 3rd, Truong L, Ferré-D'Amaré AR. Structural Principles of
Fluorescent RNA Aptamers
. Trends Pharmacol Sci. 2017 Jul 17. pii:
S0165-6147(17)30128-1. doi: 10.1016/j.tips.2017.06.007. PubMed PMID: 28728963.

3: Liang B, Ngwuta JO, Surman S, Kabatova B, Liu X, Lingemann M, Liu X, Yang L,
Herbert R, Swerczek J, Chen M, Moin SM, Kumar A, McLellan JS, Kwong PD, Graham
BS, Collins PL, Munir S. Improved Prefusion Stability, Optimized Codon Usage, and
Augmented Virion Packaging Enhance the Immunogenicity of Respiratory Syncytial
Virus Fusion Protein in a Vectored-Vaccine Candidate
. J Virol. 2017 Jul
12;91(15). pii: e00189-17. doi: 10.1128/JVI.00189-17. Print 2017 Aug 1. PubMed
PMID: 28539444.

4: Zou Z, Misasi J, Sullivan N,
Sun PD. Overexpression of Ebola virus envelope
GP1 protein
. Protein Expr Purif. 2017 Jul;135:45-53. doi:
10.1016/j.pep.2017.04.010. Epub 2017 Apr 27. PubMed PMID: 28458053.

5: Zlotkowski K, Hewitt WM, Sinniah RS, Tropea JE, Needle D, Lountos GT, Barchi
JJ Jr, Waugh DS, Schneekloth JS Jr. A Small-Molecule Microarray Approach for the
Identification of E2 Enzyme Inhibitors in Ubiquitin-Like Conjugation Pathways
.
SLAS Discov. 2017 Jul;22(6):760-766. PubMed PMID: 28346086.

For timely listing, please send a heads-up E-mail to the Editor upon publication.
TIPS, TRICKS, METHODS - A Convenient Phasing Vehicle

Zbigniew Dauter (NCI): Selenourea: A Convenient Phasing Vehicle

Majority of novel X-ray crystal structures of proteins are currently solved using the anomalous diffraction signal provided by selenium after incorporation of selenomethionine instead of natural methionine by genetic engineering methods. However, selenium can be also inserted into protein crystals in the form of selenourea (SeC(NH2)2), by adding selenourea into mother liquor or cryo-solution or in the form of powder into a drop with native crystals, in analogy to the classic procedure of heavy-atom derivatization. Selenourea is able to bind to reactive groups at the surface of macromolecules primarily through hydrogen bonds, where the selenium atom may serve as acceptor and amide groups as H-bond donors. Selenourea has different chemical properties than other heavy-atom reagents and halide ions and provides a convenient way of phasing crystal structures of macromolecules. A de novo protein crystal structure at low resolution of 2.9 Å with total 1125 residues distributed in seven chains in asymmetric unit at was recently successfully solved with this method. For details, see Selenourea: a convenient phasing vehicle for macromolecular X-ray crystal structures, Sci. Rep. 6, 37123 (2016) by Zhipu Luo.


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, NCS, Missing Atoms, Trends in CrystallographyAbsorption Correction, Data for Refinement and Publication.

LECTURES AND TUTORIALS - X-RAY CRYSTALLOGRAPHY
           
A Glimpse of Structural Biology through X-Ray 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)

NATIVE SAD IS MATURING (2015)

LITERATURE ON CRYSTALLOGRAPHY THEORY AND METHODS (2017)

PROTEIN CRYSTALLOGRAPHY Methods and Protocols (2017)

 LINKS - New Server: RestraintLib
  

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)