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Newsletter No. 336
June 20, 2016

ACA News, IUCr Newsletter, IUCr Meetings List

MAY 2016 PUBLICATIONS BY MEMBERS OF THE GROUP  


1: Li H, Wang S, Kong R, Ding W, Lee FH, Parker Z, Kim E, Learn GH, Hahn P,
Policicchio B, Brocca-Cofano E, Deleage C, Hao X, Chuang GY, Gorman J, Gardner M,
Lewis MG, Hatziioannou T, Santra S, Apetrei C, Pandrea I, Alam SM, Liao HX, Shen
X, Tomaras GD, Farzan M, Chertova E, Keele BF, Estes JD, Lifson JD, Doms RW,
Montefiori DC, Haynes BF, Sodroski JG,
Kwong PD, Hahn BH, Shaw GM. Envelope
residue 375 substitutions in simian-human immunodeficiency viruses enhance CD4
binding and replication in rhesus macaques
. Proc Natl Acad Sci U S A. 2016 May
31. pii: 201606636. [Epub ahead of print] PubMed PMID: 27247400.

2: Sliwiak J, Dauter Z, Jaskolski M. Crystal Structure of Hyp-1, a Hypericum
perforatum PR-10 Protein, in Complex with Melatonin
. Front Plant Sci. 2016 May
18;7:668. doi: 10.3389/fpls.2016.00668. eCollection 2016. PubMed PMID: 27242869;
PubMed Central PMCID: PMC4870859.

3: Rupp B,
Wlodawer A, Minor W, Helliwell JR, Jaskolski M. Correcting the record
of structural publications requires joint effort of the community and journal
editors
. FEBS J. 2016 May 26. doi: 10.1111/febs.13765. [Epub ahead of print]
Review. PubMed PMID: 27229767.

4: Sheng Z, Schramm CA, Connors M, Morris L, Mascola JR,
Kwong PD, Shapiro L.
Effects of Darwinian Selection and Mutability on Rate of Broadly Neutralizing
Antibody Evolution during HIV-1 Infection
. PLoS Comput Biol. 2016 May
18;12(5):e1004940. doi: 10.1371/journal.pcbi.1004940. eCollection 2016 May.
PubMed PMID: 27191167; PubMed Central PMCID: PMC4871536.

5: Hickman AB, Dyda F. DNA Transposition at Work. Chem Rev. 2016 May 17. [Epub
ahead of print] PubMed PMID: 27187082.

6: Kong R, Xu K, Zhou T, Acharya P, Lemmin T, Liu K, Ozorowski G, Soto C, Taft
JD, Bailer RT, Cale EM, Chen L, Choi CW, Chuang GY, Doria-Rose NA, Druz A,
Georgiev IS, Gorman J, Huang J, Joyce MG, Louder MK, Ma X, McKee K, O'Dell S,
Pancera M, Yang Y, Blanchard SC, Mothes W, Burton DR, Koff WC, Connors M, Ward
AB,
Kwong PD, Mascola JR. Fusion peptide of HIV-1 as a site of vulnerability to
neutralizing antibody
. Science. 2016 May 13;352(6287):828-33. doi:
10.1126/science.aae0474. PubMed PMID: 27174988.

7: Botos I, Majdalani N, Mayclin SJ, McCarthy JG, Lundquist K, Wojtowicz D,
Barnard TJ, Gumbart JC, Buchanan SK. Structural and Functional Characterization
of the LPS Transporter LptDE from Gram-Negative Pathogens
. Structure. 2016 May 3.
pii: S0969-2126(16)30043-0. doi: 10.1016/j.str.2016.03.026. [Epub ahead of print]
PubMed PMID: 27161977.

8: Xu B, Luo Z, Wilson AJ, Chen K, Gao W, Yuan G, Chopra HD, Chen X, Willets KA,
Dauter Z, Ren S. Multifunctional Charge-Transfer Single Crystals through
Supramolecular Assembly
. Adv Mater. 2016 May 4. doi: 10.1002/adma.201600383.
[Epub ahead of print] PubMed PMID: 27146726.

9:
Dauter Z. Objective evaluation of radiation damage in a nucleoprotein complex.
Acta Crystallogr D Struct Biol. 2016 May 1;72(Pt 5):601-2. doi:
10.1107/S2059798316006550. Epub 2016 Apr 28. PubMed PMID: 27139623.

For timely listing, please send a heads-up E-mail to the Editor upon publication.
TIPS, TRICKS, METHODS - Data Completeness from HKL2000 or HKL3000

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 - Suggestions?     

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  

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)