A new MR-SAD algorithm for the automatic building of protein models from low-resolution X-ray data and a poor starting model

Determining macromolecular structures from X-ray data with resolution worse than 3 Å remains a challenge. Even if a related starting model is available, its incompleteness or its bias together with a low observation-to-parameter ratio can render the process unsuccessful or very time-consuming. Yet, many biologically important macromolecules, especially large macromolecular assemblies, membrane proteins and receptors, tend to provide crystals that diffract to low resolution. A new algorithm to tackle this problem is presented that uses a multivariate function to simultaneously exploit information from both an initial partial model and low-resolution single-wavelength anomalous diffraction data. The new approach has been used for six challenging structure determinations, including the crystal structures of membrane proteins and macromolecular complexes that have evaded experts using other methods, and large structures from a 3.0 Å resolution F1-ATPase data set and a 4.5 Å resolution SecYEG–SecA complex data set. All of the models were automatically built by the method to Rfree values of between 28.9 and 39.9% and were free from the initial model bias

The CCP4 suite : integrative software for macromolecular crystallography

The Collaborative Computational Project No. 4 (CCP4) is a UK-led international collective with a mission to develop, test, distribute and promote software for macromolecular crystallography. The CCP4 suite is a multiplatform collection of programs brought together by familiar execution routines, a set of common libraries and graphical interfaces. The CCP4 suite has experienced several considerable changes since its last reference article, involving new infrastructure, original programs and graphical interfaces. This article, which is intended as a general literature citation for the use of the CCP4 software suite in structure determination, will guide the reader through such transformations, offering a general overview of the new features and outlining future developments. As such, it aims to highlight the individual programs that comprise the suite and to provide the latest references to them for perusal by crystallographers around the world

(4S,1\u27R)-Diethyl 6-methyl-2-[(1\u27-phenylethylimino)methyl]-4-(2-thienyl)-1,4-dihydropyridine-3,5-dicarboxylate

The absolute configuration of the title compound, C25H28N2O4S, has been determined. The molecules are interconnected by weak C-H...O hydrogen bonds. The 1,4-dihydropyridine (1,4-DHP) ring adopts the usual shallow boat conformation. The thiophene ring is nearly planar

(4R,1\u27S)-Diethyl 6-methyl-2-[(1\u27-phenylethylimino)methyl]-4-(2-thienyl)-1,4-dihydropyridine-3,5-dicarboxylate

The absolute configuration of the title compound, C25H28N2O4S, has been determined. The 1,4-dihydropyridine (1,4-DHP) ring has the usual shallow boat conformation. The thiophene ring is approximately perpendicular to the plane through the four atoms of the base of the boat. The two ester groups are twisted in the same direction and have a cis,cis geometry with respect to the adjacent ring double bonds

(4R,1\u27S)-Diethyl 6-methyl-2-[(1\u27-phenylethylimino)methyl]-4-(2-thienyl)-1,4-dihydropyridine-3,5-dicarboxylate

The absolute configuration of the title compound, C25H28N2O4S, has been determined. The 1,4-dihydropyridine (1,4-DHP) ring has the usual shallow boat conformation. The thiophene ring is approximately perpendicular to the plane through the four atoms of the base of the boat. The two ester groups are twisted in the same direction and have a cis,cis geometry with respect to the adjacent ring double bonds

The CCP4 suite: integrative software for macromolecular crystallography.

Funder: European Molecular Biology LaboratoryThe Collaborative Computational Project No. 4 (CCP4) is a UK-led international collective with a mission to develop, test, distribute and promote software for macromolecular crystallography. The CCP4 suite is a multiplatform collection of programs brought together by familiar execution routines, a set of common libraries and graphical interfaces. The CCP4 suite has experienced several considerable changes since its last reference article, involving new infrastructure, original programs and graphical interfaces. This article, which is intended as a general literature citation for the use of the CCP4 software suite in structure determination, will guide the reader through such transformations, offering a general overview of the new features and outlining future developments. As such, it aims to highlight the individual programs that comprise the suite and to provide the latest references to them for perusal by crystallographers around the world

The CCP4 suite: integrative software for macromolecular crystallography.

The Collaborative Computational Project No. 4 (CCP4) is a UK-led international collective with a mission to develop, test, distribute and promote software for macromolecular crystallography. The CCP4 suite is a multiplatform collection of programs brought together by familiar execution routines, a set of common libraries and graphical interfaces. The CCP4 suite has experienced several considerable changes since its last reference article, involving new infrastructure, original programs and graphical interfaces. This article, which is intended as a general literature citation for the use of the CCP4 software suite in structure determination, will guide the reader through such transformations, offering a general overview of the new features and outlining future developments. As such, it aims to highlight the individual programs that comprise the suite and to provide the latest references to them for perusal by crystallographers around the world