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Newsletter No. 341
September 5, 2016

Sad news, David Davies, 1927-2016 

(September 2, 2016)

     

ACA News, IUCr Newsletter, IUCr Meetings List

AUGUST 2016 PUBLICATIONS BY MEMBERS OF THE GROUP  


1: Wibmer CK, Gorman J, Anthony CS, Mkhize NN, Druz A, York T, Schmidt SD,
Labuschagne P, Louder MK, Bailer RT, Abdool Karim SS, Mascola JR, Williamson C,
Moore PL,
Kwong PD, Morris L. Structure of an N276-dependent HIV-1 Neutralizing
Antibody Targeting a Rare V5 Glycan Hole adjacent to the CD4 Binding Site
. J
Virol. 2016 Aug 31. pii: JVI.01357-16. [Epub ahead of print] PubMed PMID:
27581986.

2: Liang B, Ngwuta JO, Herbert R, Swerczek J, Dorward DW, Amaro-Carambot E,
Mackow N, Kabatova B, Lingemann M, Surman S, Yang L, Chen M, Moin SM, Kumar A,
McLellan JS,
Kwong PD, Graham BS, Schaap-Nutt A, Collins PL, Munir S. Packaging
and prefusion stabilization separately and additively increase the quantity and
quality of RSV-neutralizing antibodies induced by respiratory syncytial virus
(RSV) fusion protein expressed by a parainfluenza vector
. J Virol. 2016 Aug 31.
pii: JVI.01196-16. [Epub ahead of print] PubMed PMID: 27581977.

3: Hashiguchi T, Arakawa S, Takahashi S, Gonzalez FJ, Sueyoshi T, Negishi M.
Phosphorylation of farnesoid X receptor at serine 154 links ligand activation
with degradation
. Mol Endocrinol. 2016 Aug 29:me20161105. [Epub ahead of print]
PubMed PMID: 27571290.

4:
Esser L, Shukla S, Zhou F, Ambudkar SV, Xia D. Crystal structure of the
antigen-binding fragment of a monoclonal antibody specific for the
multidrug-resistance-linked ABC transporter human P-glycoprotein
. Acta
Crystallogr F Struct Biol Commun. 2016 Aug 1;72(Pt 8):636-41. doi:
10.1107/S2053230X16009778. Epub 2016 Jul 27. PubMed PMID: 27487928; PubMed
Central PMCID: PMC4973305.

5: Pletneva NV, Pletnev S, Pakhomov AA, Chertkova RV, Martynov VI, Muslinkina L,
Dauter Z, Pletnev VZ. Crystal structure of the fluorescent protein from
Dendronephthya sp. in both green and photoconverted red forms
. Acta Crystallogr D
Struct Biol. 2016 Aug 1;72(Pt 8):922-32. doi: 10.1107/S205979831601038X. Epub
2016 Jul 13. PubMed PMID: 27487823; PubMed Central PMCID: PMC4973210.

6: Joyce MG, Zhang B, Ou L, Chen M, Chuang GY, Druz A, Kong WP, Lai YT, Rundlet
EJ, Tsybovsky Y, Yang Y, Georgiev IS, Guttman M, Lees CR, Pancera M, Sastry M,
Soto C, Stewart-Jones GB, Thomas PV, Van Galen JG, Baxa U, Lee KK, Mascola JR,
Graham BS,
Kwong PD. Iterative structure-based improvement of a
fusion-glycoprotein vaccine against RSV
. Nat Struct Mol Biol. 2016 Aug 1. doi:
10.1038/nsmb.3267. [Epub ahead of print] PubMed PMID: 27478931.

For timely listing, please send a heads-up E-mail to the Editor upon publication.
TIPS, TRICKS, METHODS Restraint Libraries for Nucleic Acids

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.


Xinhua Ji (NCI): Phenix Tool For Omit Map Calculation

Phenix.polder calculates omit maps for selected atoms while preventing the bulk solvent mask to flood into the selected area and its vicinity. The tool can be useful in cases where the density of selected atoms is weak and possibly obscured by bulk solvent.

Usage
phenix.polder  model.pdb  data.mtz  selection='chain A and resseq 123'

Examples
https://www.phenix-online.org/presentations/phenix_polder.pdf

Documentation

http://www.phenix-online.org/version_docs/dev-2356/reference/polder.html


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.

Mariusz Jaskolski: Geometrical Restraints of His Residues
A recent paper, already listed on this bulletin board, will give you a hint about improving the geometrical restraints of His residues, depending on their protonation/tautomeric form, especially at high resolution:

M.Malinska, M.Dauter, M.Kowiel, M.Jaskolski, Z.Dauter (2015) Protonation and geometry of histidine rings. Acta Cryst. D71, 1444-1454.

This may be a good occasion to mention that for years Refmac has been using the older (1991) version (containing errors) of the Engh & Huber stereochemical dictionary, even though the authors themselves (E&H) corrected it in 2001...

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 - Dr. Dauter's Lectures Are Back!

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)

 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)