Newsletter 181
October 20, 2008


The NIH X-Ray Diffraction Interest Group

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

Special Item: Photos and Reports of IUCr 2008

     

Item 1: September 2008 Publications by Members of the Group 

1: Xiao T.
 Innate immune recognition of nucleic acids.
Immunol Res. 2008 Sep 23. PMID: 18810334
    
2: Sobhany M, Kakuta Y, Sugiura N, Kimata K, Negishi M.
 The chondroitin polymerase K4CP: Molecular mechanism of selective 
bindings of donor substrates to two active sites.
J Biol Chem. 2008 Sep 19. PMID: 18806260 
    
3: Shaw G, Gan J, Zhou YN, Zhi H, Subburaman P, Zhang R, Joachimiak A,
Jin DJ, Ji X.
 Structure of RapA, a Swi2/Snf2 protein that recycles RNA polymerase 
during transcription.
Structure. 2008 Sep 10;16(9):1417-27. PMID: 18786404
    
4: Klein MM, Gittis AG, Su HP, Makobongo MO, Moore JM, Singh S, Miller LH,
Garboczi DN.
 The cysteine-rich interdomain region from the highly variable plasmodium
falciparum erythrocyte membrane protein-1 exhibits a conserved structure.
PLoS Pathog. 2008 Sep 5;4(9):e1000147. PMID: 18773118 
    
5: Doucleff M, Clore GM.
 Global jumping and domain-specific intersegment transfer between DNA cognate
sites of the multidomain transcription factor Oct-1.
Proc Natl Acad Sci U S A. 2008 Sep 16;105(37):13871-6. PMID: 18772384

Item 2: Tips and Tricks

Item 3: Topic Discussion - Validation

Mariusz Jaskolski (CBR): Ultra-High Resolution Structures in Validation

    Abstract: In variance with small-molecule crystallography, where structure refinement is highly overdetermined by a large surplus of diffraction data, the observation/parameter ratio in macromolecular crystallography is usually low and only at about 2.7-2.5 Å resolution reaches 1.0 for reasonably constructed models. It is, therefore, not only useful but mathematically necessary to use stereochemical restraints in macromolecular refinement at low resolution. At higher resolution the restraints are still used, for a variety of reasons, but at some point, usually when atomic resolution (1.2 Å) has been reached, they may be relaxed as the diffraction terms are "taking the refinement over". It is a valid question, however, if the restraints could be dropped altogether, and if yes, under what conditions. A separate question concerns the restraint targets themselves and the strictness with which they should be obeyed. The most popular library of stereochemical standards was compiled in 1991 by Engh and Huber from careful analysis of small-molecule structures available at that time in the Cambridge Structural Database (CSD). A survey of the entries deposited in the Protein Data Bank (PDB) indicates that often the models are forced to imitate the standards more closely than justified by the errors with which those standards were originally estimated. Additionally, with a nearly six-fold expansion of the CSD from 80,000 entries in 1991, it might be interesting to see if the "old" stereochemical standards are still valid. An even more interesting possibility is opened up by the explosive growth of the PDB (100-fold since 1990), now holding more than 52,000 entries, and especially by the rapid accumulation of ultra-high resolution protein structures. For example, 0.8 Å resolution macromolecular structures were unknown in 1997, while today there are about two dozen of them. Such structures are usually refined with utmost care and are only minimally "contaminated" by the prior knowledge enforced by stereochemical restraints. They offer, therefore, a unique possibility to review (and if necessary to adjust) the stereochemical standards of protein structure. A preliminary analysis indicates that while some of the "old" standards have withstood the test of time, some others might need small but clear adjustments. This is especially true of the peptide group, which can show higher deviations (up to 20º) from strict planarity than allowed by the restraints. It is also important conceptually that we are now able to obtain "protein parameters from proteins". With the currently attainable level of accuracy, one can investigate if there are any detectable idiosyncrasies of protein structure, related for instance to the specific nature of protein conformation or to specific interactions with the environment. Finally, the parameters derived from ultra-high resolution protein structures can serve not only as more appropriate stereochemical targets for model refinement but may also be used as validation criteria for lower resolution models. (Presentation)

     

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).