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Newsletter No. 338
July 18, 2016

Dr. Zbigniew Dauter Selected to Receive the 2017 ACA Patterson Award

Congratulations!

ACA News, IUCr Newsletter, IUCr Meetings List

JUNE 2016 PUBLICATIONS BY MEMBERS OF THE GROUP  


1: Malinska M, Dauter M, Dauter Z. Geometry of guanidinium groups in arginines.
Protein Sci. 2016 Jun 21. doi: 10.1002/pro.2970. [Epub ahead of print] PubMed
PMID: 27326702.

2: Malinska M,
Dauter Z. Transferable aspherical atom model refinement of protein
and DNA structures against ultrahigh-resolution X-ray data
. Acta Crystallogr D
Struct Biol. 2016 Jun 1;72(Pt 6):770-9. doi: 10.1107/S2059798316006355. Epub 2016
May 25. PubMed PMID: 27303797; PubMed Central PMCID: PMC4908868.

3: Soto C, Ofek G, Joyce MG, Zhang B, McKee K, Longo NS, Yang Y, Huang J, Parks
R, Eudailey J, Lloyd KE, Alam SM, Haynes BF; NISC Comparative Sequencing Program,
Mullikin JC, Connors M, Mascola JR, Shapiro L,
Kwong PD. Developmental Pathway of
the MPER-Directed HIV-1-Neutralizing Antibody 10E8
. PLoS One. 2016 Jun
14;11(6):e0157409. doi: 10.1371/journal.pone.0157409. eCollection 2016. PubMed
PMID: 27299673.

4: Gao Y, Yang W. Capture of a third Mg²⁺ is essential for catalyzing DNA
synthesis
. Science. 2016 Jun 10;352(6291):1334-7. doi: 10.1126/science.aad9633.
PubMed PMID: 27284197.

5: Ruszkowski M,
Dauter Z. On methylene-bridged cysteine and lysine residues in
proteins
. Protein Sci. 2016 Jun 4. doi: 10.1002/pro.2958. [Epub ahead of print]
PubMed PMID: 27261771.

6: Kwon YD, Georgiev IS, Ofek G, Zhang B, Asokan M, Bailer RT, Bao A, Caruso W,
Chen X, Choe M, Druz A, Ko SY, Louder MK, McKee K, O'Dell S, Pegu A, Rudicell RS,
Shi W, Wang K, Yang Y, Alger M, Bender MF, Carlton K, Cooper JW, Blinn J,
Eudailey J, Lloyd K, Parks R, Alam SM, Haynes BF, Padte NN, Yu J, Ho DD, Huang J,
Connors M, Schwartz RM, Mascola JR,
Kwong PD. Optimization of the Solubility of
HIV-1-Neutralizing Antibody 10E8 through Somatic Variation and Structure-Based
Design
. J Virol. 2016 Jun 10;90(13):5899-914. doi: 10.1128/JVI.03246-15. Print
2016 Jul 1. PubMed PMID: 27053554; PubMed Central PMCID: PMC4907239.

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)