e16.html

1: Tozser J, Tropea JE, Cherry S, Bagossi P, Copeland TD, Wlodawer A, Waugh DS.
Comparison of the substrate specificity of two potyvirus proteases.
FEBS J. 2005 Jan;272(2):514-23. PMID: 15654889

2: Qasba PK, Ramakrishnan B, Boeggeman E.
Substrate-induced conformational changes in glycosyltransferases.
Trends Biochem Sci. 2005 Jan;30(1):53-62. PMID: 15653326

3: Baker T, Dauter Z.
Redefining Acta D.
Acta Crystallogr D Biol Crystallogr. 2005 Jan;61(Pt 1):1. PMID: 15608369

4: Gozansky EK, Louis JM, Caffrey M, Clore GM.
Mapping the binding of the N-terminal extracellular tail of the CXCR4 receptor to stromal cell-derived factor-1alpha.
J Mol Biol. 2005 Jan 28;345(4):651-8. PMID: 15588815

Lothar Esser (NCI): The Successor of BEAST - Molecular replacement is always a bit tricky especially with poor data. The membrane protein that I work on provides only very anisotropic data and the only program that could handle it was the successor of BEAST: Phaser. So many people have said so many good things about phaser ( see G. Sheldrick's comments on the CCP4BB ) that I do not need to add anything only so much that it solved my difficult problem too. I have a solution despite less than ideal data. What usually convinces me of the correctness of a solution is when I see peaks in the anomalous difference map for sulfur atoms or atoms of which Z>=16. Just to be on the safe side, my MR models are usually free of S or any heavy atoms so that when I get peaks in the right places, I am convinced. Coming back to data, Phaser rejects outliers also but its great strength (at least in my case) lies in the correction of anisotropic data. I'd highly recommend it.

Xinhua Ji (NCI): The Beauty of BEAST - Outliers among diffraction data are usually of lower resolution and relatively stronger and thereby have greater impact on the functions derived from intensities. One consequence of this impact is the lack of phasing power of molecular replacement (MR) solution. We recently encountered this problem with an MR solution obtained using a search model equivalent to ~50% the structure. With AMoRe, we found an solution; but we were not able to complete the structure using either the difference Fourier synthesis or other programs. Assuming that the MR solution was not accurate, we tried MR again excluding potential outliers. BEAST identified 22 potential outliers and rejected them from likelihood calculations. The MR solution was outstanding and the difference map derived from the partial structure reveals the missing portion of the structure.