Protein phasing at non-atomic resolution by combining Patterson and<i>VLD</i>techniques

Caliandro, Rocco; Carrozzini, Benedetta; Cascarano, G.; Comunale, Giuliana; Giacovazzo, Carmelo; Mazzone, A.

doi:10.1107/s139900471401013x

Cited by 11 publications

(13 citation statements)

References 47 publications

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“…The procedure has been favourably tested by 126 macromolecules with data resolution varying from atomic up to 2.1 Å , under the condition that S or heavier atoms are present in the structures. It has been shown that computer programs protein structures may be automatically solved even when the data resolution is close to 2 Å (Caliandro et al, 2014). The figures of merit fFOM and fFOM2 defined above are used to recognize the correct solutions and to stop the program.…”

Section: Patterson Deconvolution Proceduresmentioning

confidence: 99%

Crystal structure determination and refinementviaSIR2014

et al. 2015

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SIR2014 is the latest program of the SIR suite for crystal structure solution of small, medium and large structures. A variety of phasing algorithms have been implemented, both ab initio (standard or modern direct methods, Patterson techniques, Vive la Différence) and non-ab initio (simulated annealing, molecular replacement). The program contains tools for crystal structure refinement and for the study of three-dimensional electron-density maps via suitable viewers.

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Section: Patterson Deconvolution Proceduresmentioning

confidence: 99%

Crystal structure determination and refinementviaSIR2014

et al. 2015

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“…In combination with EDM techniques, VLD has been successfully applied (Burla et al, 2011;Carrozzini et al, 2013;Caliandro et al, 2014) for ab initio crystal structure solution of small and medium-size molecules, for ab initio phasing of proteins with data at atomic resolution and with heavy atoms in the unit cell, and for phase refinement of models arising from MR. The typical procedure may be schematized as follows.…”

Section: Oedm Techniquesmentioning

confidence: 99%

Synergy among phase-refinement techniques in macromolecular crystallography

Burla

Cascarano

Giacovazzo

et al. 2017

Acta Cryst Sect D Struct Biol

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Ab initio and non-ab initio phasing methods are often unable to provide phases of sufficient quality to allow the molecular interpretation of the resulting electron-density maps. Phase extension and refinement is therefore a necessary step: its success or failure can make the difference between solution and nonsolution of the crystal structure. Today phase refinement is trusted to electron-density modification (EDM) techniques, and in practice to dual-space methods which try, via suitable constraints in direct and in reciprocal space, to generate higher quality electron-density maps. The most popular EDM approaches, denoted here as mainstream methods, are usually part of packages which assist crystallographers in all of the structure-solution steps from initial phasing to the point where the molecular model perfectly fits the known features of protein chemistry. Other phase-refinement approaches that are based on different sources of information, denoted here as out-of-mainstream methods, are not frequently employed. This paper aims to show that mainstream and out-of-mainstream methods may be combined and may lead to dramatic advances in the present state of the art. The statement is confirmed by experimental tests using molecular-replacement, SAD-MAD and ab initio techniques.

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“…(i) DM (Cowtan, 1994(Cowtan, , 1999; available from CCP4; Winn et al, 2011) for electron-density modification of structures with data resolution worse than 1.25 Å and DSR (Giacovazzo & Siliqi, 1997;Caliandro et al, 2014) for higher resolution diffraction data.…”

Section: The Phasing Proceduresmentioning

confidence: 99%

Phase improvementviathePhantom Derivativetechnique: ancils that are related to the target structure

Carrozzini

Cascarano

Giacovazzo

2016

Acta Cryst Sect D Struct Biol

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Density modification is a general standard technique which may be used to improve electron density derived from experimental phasing and also to refine densities obtained by ab initio approaches. Here, a novel method to expand density modification is presented, termed the Phantom derivative technique, which is based on non-existent structure factors and is of particular interest in molecular replacement. The Phantom derivative approach uses randomly generated ancil structures with the same unit cell as the target structure to create non-existent derivatives of the target structure, called phantom derivatives, which may be used for ab initio phasing or for refining the available target structure model. In this paper, it is supposed that a model electron density is available: it is shown that ancil structures related to the target obtained by shifting the target by origin-permissible translations may be employed to refine model phases. The method enlarges the concept of the ancil, is as efficient as the canonical approach using random ancils and significantly reduces the CPU refinement time. The results from many real test cases show that the proposed methods can substantially improve the quality of electron-density maps from molecular-replacement-based phases.

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Protein phasing at non-atomic resolution by combining Patterson andVLDtechniques

Cited by 11 publications

References 47 publications

Crystal structure determination and refinementviaSIR2014

Crystal structure determination and refinementviaSIR2014

Synergy among phase-refinement techniques in macromolecular crystallography

Phase improvementviathePhantom Derivativetechnique: ancils that are related to the target structure

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