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Newsletter No. 352
April 3, 2017

ACA News, IUCr Newsletter, IUCr Meetings List

MARCH 2017 PUBLICATIONS BY MEMBERS OF THE GROUP  

1: Alam SM, Aussedat B, Vohra Y, Ryan Meyerhoff R, Cale EM, Walkowicz WE,
Radakovich NA, Anasti K, Armand L, Parks R, Sutherland L, Scearce R, Joyce MG,
Pancera M, Druz A, Georgiev IS, Von Holle T, Eaton A, Fox C, Reed SG, Louder M,
Bailer RT, Morris L, Abdool-Karim SS, Cohen M, Liao HX, Montefiori DC, Park PK,
Fernández-Tejada A, Wiehe K, Santra S, Kepler TB, Saunders KO, Sodroski J, Kwong
PD
, Mascola JR, Bonsignori M, Moody MA, Danishefsky S, Haynes BF. Mimicry of an
HIV broadly neutralizing antibody epitope with a synthetic glycopeptide
. Sci
Transl Med. 2017 Mar 15;9(381). pii: eaai7521. doi: 10.1126/scitranslmed.aai7521.
PubMed PMID: 28298421.

2: Chuang GY, Geng H, Pancera M, Xu K, Cheng C, Acharya P, Chambers M, Druz A,
Tsybovsky Y, Wanninger TG, Yang Y, Doria-Rose NA, Georgiev IS, Gorman J, Joyce
MG, O'Dell S, Zhou T, McDermott AB, Mascola JR,
Kwong PD. Structure-Based Design
of a Soluble Prefusion-Closed HIV-1-Env Trimer with Reduced CD4 Affinity and
Improved Immunogenicity
. J Virol. 2017 Mar 8. pii: JVI.02268-16. doi:
10.1128/JVI.02268-16. [Epub ahead of print] PubMed PMID: 28275193.

3: Curreli F, Kwon YD, Belov DS, Ramesh RR, Kurkin AV, Altieri A,
Kwong PD,
Debnath AK. Synthesis, Antiviral Potency, in Vitro ADMET, and X-ray Structure of
Potent CD4 Mimics as Entry Inhibitors That Target the Phe43 Cavity of HIV-1
gp120
. J Med Chem. 2017 Mar 16. doi: 10.1021/acs.jmedchem.7b00179. [Epub ahead of
print] PubMed PMID: 28266845.

4: Shizu R, Osabe M, Perera L, Moore R, Sueyoshi T, Negishi M. Phosphorylated
nuclear receptor CAR forms a homodimer to repress its constitutive activity for
ligand activation
. Mol Cell Biol. 2017 Mar 6. pii: MCB.00649-16. doi:
10.1128/MCB.00649-16. [Epub ahead of print] PubMed PMID: 28265001.

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)