Journal ArticleDOI
Substructure solution with SHELXD.
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TLDR
Iterative dual-space direct methods based on phase refinement in reciprocal space and peak picking in real space are able to locate relatively large numbers of anomalous scatterers efficiently from MAD or SAD data.Abstract:
Iterative dual-space direct methods based on phase refinement in reciprocal space and peak picking in real space are able to locate relatively large numbers of anomalous scatterers efficiently from MAD or SAD data. Truncation of the data at a particular resolution, typically in the range 3.0–3.5 A, can be critical to success. The efficiency can be improved by roughly an order of magnitude by Patterson-based seeding instead of starting from random phases or sites; Patterson superposition methods also provide useful validation. The program SHELXD implementing this approach is available as part of the SHELX package.read more
Citations
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Journal ArticleDOI
A short history of SHELX
TL;DR: This paper could serve as a general literature citation when one or more of the open-source SH ELX programs (and the Bruker AXS version SHELXTL) are employed in the course of a crystal-structure determination.
Journal ArticleDOI
Crystal structure refinement with SHELXL
TL;DR: New features added to the refinement program SHELXL since 2008 are described and explained.
Journal ArticleDOI
Linking crystallographic model and data quality.
P. Andrew Karplus,Kay Diederichs +1 more
TL;DR: Here, it is shown that despite their widespread use, Rmerge values are poorly suited for determining the high-resolution limit and that current standard protocols discard much useful data, and a statistic is introduced that estimates the correlation of an observed data set with the underlying (not measurable) true signal.
Journal ArticleDOI
Experimental phasing with SHELXC/D/E: combining chain tracing with density modification
TL;DR: Experimental phasing with SHELXC/D/E has been enhanced by the incorporation of main-chain tracing into the iterative density modification; this also provides a simple and effective way of exploiting noncrystallographic symmetry.
Journal ArticleDOI
Structures of Cas9 Endonucleases Reveal RNA- Mediated Conformational Activation
Martin Jinek,Fuguo Jiang,David W. Taylor,David W. Taylor,Samuel H. Sternberg,Emine Kaya,Enbo Ma,Carolin Anders,Michael H. Hauer,Kaihong Zhou,Steven Lin,Matias Kaplan,Anthony T. Iavarone,Emmanuelle Charpentier,Emmanuelle Charpentier,Eva Nogales,Jennifer A. Doudna +16 more
TL;DR: To compare the architectures and domain organization of diverse Cas9 proteins, the atomic structures of Cas9 from Streptococcus pyogenes and Actinomyces naeslundii and AnaCas9 were determined by x-ray crystallography and three-dimensional reconstructions of apo-SpyCas9, SpyCas9:RNA, and SpyCas 9:RNA:DNA were obtained by negative-stain single-particle electron microscopy.
References
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Journal ArticleDOI
Phase annealing in SHELX-90: direct methods for larger structures
TL;DR: In this article, a phase annealing method, related to the simulated-annealing approach in other optimization problems, is proposed and it is shown that it can result in an improvement of up to an order of magnitude in the chances of solving large structures at atomic resolution.
Journal ArticleDOI
Free R value: a novel statistical quantity for assessing the accuracy of crystal structures.
TL;DR: In this article, a statistical quantity (RfreeT) is defined to measure the agreement between observed and computed structure factor amplitudes for a 'test' set of reflections that is omitted in the modelling and refinement process.
Journal ArticleDOI
Determination of Macromolecular Structures from Anomalous Diffraction of Synchrotron Radiation
TL;DR: The problem of determining the three-dimensional structure of thousands of atoms is reduced to that of initially solving for a few anomalous scattering centers that can be used as a reference for developing the entire structure.
Journal ArticleDOI
Model bias in macromolecular crystal structures
TL;DR: In this paper, a reduction of model bias in macromolecular crystallography through various omit-map techniques has been investigated, including simulated-annealing refinement and conjugate-gradient minimization.
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