logo2a.gif

Newsletter No. 351
March 20, 2017

ACA News, IUCr Newsletter, IUCr Meetings List

FEBRUARY 2017 PUBLICATIONS BY MEMBERS OF THE GROUP  


1: Ghequire MG, Kemland L, Anoz-Carbonell E, Buchanan SK, De Mot R. A Natural
Chimeric Pseudomonas Bacteriocin with Novel Pore-Forming Activity Parasitizes the
Ferrichrome Transporter
. MBio. 2017 Feb 21;8(1). pii: e01961-16. doi:
10.1128/mBio.01961-16. PubMed PMID: 28223456.

2: Liu Q, Acharya P, Dolan MA, Zhang P, Guzzo C, Lu J, Kwon A, Gururani D, Miao
H, Bylund T, Chuang GY, Druz A, Zhou T, Rice WJ, Wigge C, Carragher B, Potter CS,
Kwong PD, Lusso P. Quaternary contact in the initial interaction of CD4 with the
HIV-1 envelope trimer
. Nat Struct Mol Biol. 2017 Feb 20. doi: 10.1038/nsmb.3382.
[Epub ahead of print] PubMed PMID: 28218750.

3: Noinaj N, Gumbart JC,
Buchanan SK. The β-barrel assembly machinery in motion.
Nat Rev Microbiol. 2017 Apr;15(4):197-204. doi: 10.1038/nrmicro.2016.191. Review.
PubMed PMID: 28216659.

4: Luo Z, Dauter Z. Embarras de richesses - It is not good to be too anomalous:
Accurate structure of selenourea, a chiral crystal of planar molecules
. PLoS One.
2017 Feb 16;12(2):e0171740. doi: 10.1371/journal.pone.0171740. PubMed PMID:
28207770; PubMed Central PMCID: PMC5313157.

5: Pancera M, Changela A,
Kwong PD. How HIV-1 entry mechanism and broadly
neutralizing antibodies guide structure-based vaccine design
. Curr Opin HIV AIDS.
2017 Feb 15. doi: 10.1097/COH.0000000000000360. [Epub ahead of print] PubMed
PMID: 28207490.

6: Horton JK, Seddon HJ, Zhao ML, Gassman NR, Janoshazi AK, Stefanick DF, Wilson
SH
. Role of the oxidized form of XRCC1 in protection against extreme oxidative
stress
. Free Radic Biol Med. 2017 Feb 4. pii: S0891-5849(17)30066-7. doi:
10.1016/j.freeradbiomed.2017.02.005. [Epub ahead of print] Review. PubMed PMID:
28179111.


7: Shahzad-Ul-Hussan S, Sastry M, Lemmin T, Soto C, Loesgen S, Scott DA, Davison
JR, O'Connor R,
Kwong PD, Bewley CA. NMR insights into the conformational
properties of Man-9 and its recognition by two HIV binding proteins
. Chembiochem.
2017 Feb 6. doi: 10.1002/cbic.201600665. [Epub ahead of print] PubMed PMID:
28166380.

8:
Kwong PD. What Are the Most Powerful Immunogen Design Vaccine Strategies? A
Structural Biologist's Perspective
. Cold Spring Harb Perspect Biol. 2017 Feb 3.
pii: a029470. doi: 10.1101/cshperspect.a029470. [Epub ahead of print] PubMed
PMID: 28159876.

9: Libich DS, Tugarinov V, Ghirlando R, Clore GM. Confinement and Stabilization
of Fyn SH3 Folding Intermediate Mimetics within the Cavity of the Chaperonin
GroEL Demonstrated by Relaxation-Based NMR
. Biochemistry. 2017 Feb
21;56(7):903-906. doi: 10.1021/acs.biochem.6b01237. PubMed PMID: 28156097.

10: Lubkowski J, Durbin SV, Silva MC, Farnsworth D, Gildersleeve JC, Oliva ML,
Wlodawer A. Structural analysis and unique molecular recognition properties of a
Bauhinia forficata lectin that inhibits cancer cell growth
. FEBS J. 2017
Feb;284(3):429-450. doi: 10.1111/febs.13989. PubMed PMID: 27973758.

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)