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Electron-density Modification (electron-density + modification)

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Chemistry100%

Selected Abstracts

EDM,DEDM and protein crystal structure solution

ACTA CRYSTALLOGRAPHICA SECTION D, Issue 5 2009
Rocco Caliandro
Electron-density modification (EDM) procedures are the classical tool for driving model phases closer to those of the target structure. They are often combined with automated model-building programs to provide a correct protein model. The task is not always performed, mostly because of the large initial phase error. A recently proposed procedure combined EDM with DEDM (difference electron-density modification); the method was applied to the refinement of phases obtained by molecular replacement, ab initio or SAD phasing [Caliandro, Carrozzini, Cascarano, Giacovazzo, Mazzone & Siliqi (2009), Acta Cryst. D65, 249,256] and was more effective in improving phases than EDM alone. In this paper, a novel fully automated protocol for protein structure refinement based on the iterative application of automated model-building programs combined with the additional power derived from the EDM,DEDM algorithm is presented. The cyclic procedure was successfully tested on challenging cases for which all other approaches had failed. [source]

The (Fo,Fc) Fourier synthesis: a probabilistic study

ACTA CRYSTALLOGRAPHICA SECTION A, Issue 5 2008
Rocco Caliandro
(Fo,Fc) and (2Fo,Fc) Fourier syntheses are considered the most powerful tools for recovering the remainder of a structure and for correcting crystal structure models. A probabilistic approach has been applied to derive the formula for the variance for the expected value of the coefficient (Fo,Fc). This has allowed a better understanding of the features of the difference Fourier synthesis; in particular, a subset of well phased reflections has been separated from the subset of reflections best phased by the standard Fo Fourier synthesis. An iterative procedure, based on the electron-density modification of the difference Fourier map, has been devised which aims to improve phase and modulus estimates of the reflections with higher variance value, by using as lever arm the set of reflections with lower variance value. The new procedure (DEDM) has been implemented and verified on a wide set of test structures, the partial models of which were obtained by molecular replacement or by automatic model-building routines applied to experimental electron-density maps. Phase and modulus estimates of the difference Fourier syntheses improve in all the test cases; as a consequence, the quality of the difference Fourier maps also improves in the region where the target structure deviates from the partial model. A new procedure is suggested, combining DEDM with standard electron-density modification techniques, which leads to significant reduction of the phase errors. The procedure may be considered a starting point for further developments. [source]

EDM,DEDM and protein crystal structure solution

ACTA CRYSTALLOGRAPHICA SECTION D, Issue 5 2009
Rocco Caliandro
Electron-density modification (EDM) procedures are the classical tool for driving model phases closer to those of the target structure. They are often combined with automated model-building programs to provide a correct protein model. The task is not always performed, mostly because of the large initial phase error. A recently proposed procedure combined EDM with DEDM (difference electron-density modification); the method was applied to the refinement of phases obtained by molecular replacement, ab initio or SAD phasing [Caliandro, Carrozzini, Cascarano, Giacovazzo, Mazzone & Siliqi (2009), Acta Cryst. D65, 249,256] and was more effective in improving phases than EDM alone. In this paper, a novel fully automated protocol for protein structure refinement based on the iterative application of automated model-building programs combined with the additional power derived from the EDM,DEDM algorithm is presented. The cyclic procedure was successfully tested on challenging cases for which all other approaches had failed. [source]

Advances in the EDM,DEDM procedure

ACTA CRYSTALLOGRAPHICA SECTION D, Issue 3 2009
Rocco Caliandro
The DEDM (difference electron-density modification) algorithm has been described in a recent paper [Caliandro et al. (2008), Acta Cryst. A64, 519,528]: it breaks down the collinearity between model structure phases and difference structure phase estimates. The new difference electron-density produced by DEDM, summed to the calculated Fourier maps, is expected to provide a representation of the full structure that is more accurate than that obtained by the observed Fourier synthesis. In the same paper, the DEDM algorithm was combined with the EDM (electron-density modification) approach to give the EDM,DEDM procedure which, when applied to practical molecular-replacement cases, was able to improve the model structures. In this paper, it is shown that EDM,DEDM suffers from some critical points that did not allow cyclical application of the procedure. These points are identified and modifications are made to allow iteration of the procedure. The applications indicate that EDM,DEDM may become a fundamental tool in protein crystallography. [source]