Newsletter 177
August 11, 2008

The NIH X-Ray Diffraction Interest Group

Newsletter web site: http://mcl1.ncifcrf.gov/nihxray

21st Congress of the International Union of Crystallography 2008
23 - 31 August 2008, Osaka, Japan

Item 1: July 2008 Publications by Members of the Group

   
1: Plested AJ, Mayer ML.
 Engineering a high-affinity allosteric binding site for divalent 
cations in kainate receptors.
Neuropharmacology. 2008 Jul 18. PMID: 18687343 
  
2: Kuszewski JJ, Thottungal RA, Clore GM, Schwieters CD.
 Automated error-tolerant macromolecular structure determination 
from multidimensional nuclear Overhauser enhancement spectra and 
chemical shift assignments: improved robustness and performance 
of the PASD algorithm.
J Biomol NMR. 2008 Jul 31. PMID: 18668206 
   
3: Gustchina E, Bewley CA, Clore GM.
 Sequestering the Pre-Hairpin Intermediate of gp41 by Peptide 
N36Mut(e,g)Potentiates the Human Immunodeficiency Virus Type 1 
Neutralizing Activity of Monoclonal Antibodies Directed Against 
the N-Terminal Helical Repeat of gp41.
J Virol. 2008 Jul 30. PMID: 18667502 
   
4: Yao Y, Harrison CB, Freddolino PL, Schulten K, Mayer ML.
 Molecular mechanism of ligand recognition by NR3 subtype 
glutamate receptors.
EMBO J. 6;27(15):2158-70. Epub 2008 Jul 17. PMID: 18636091

Item 2: Tips and Tricks

phenix.refine: crystallographic structure refinement in PHENIX

Pavel V. Afonine, Ralf W. Grosse-Kunstleve, Peter H. Zwart, Thomas C. Terwilliger, Nigel W. Moriarty & Paul D. Adams

A combination of highly efficient programming tools and new or improved crystallographic algorithms provides a very high level of automation and robustness in structure refinement. Their implementation in phenix.refine – state-of-the-art refinement module of PHENIX package – resulted in a complete set of tools that cover most of refinement needs and scenarios, such as: ... (full article).

Pavel V. Afonine's recent lecture on phenix.refine (click here).

Click for Introduction and tips and tricks in Pre-crystallization modification, Crystallization, Post-crystallization treatment, Derivatization, Diffraction, Symmetry, Structure Solution, Structure Refinement, and Structure Analysis & Presentation.

Item 3: Topic Discussion

Click for previous discussions on: Twinning, Low Resolution Crystallography, PHASER, HKL2000, Parallel Protein Expression, Structural Genomics, NCS, Missing Atoms, Trends in Crystallography, and Absorption Correction.

Item 4: 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"

This site is maintained by Dr. Xinhua Ji (jix@ncifcrf.gov) on the NCI-CCR-MCL server (http://mcl1.ncifcrf.gov).