Benedetta Carrozzini

SIR2004: an improved tool for crystal structure determination and refinement

SIR2004 is the evolution of the SIR2002 program [Burla, Camalli, Carrozzini, Cascarano, Giacovazzo, Polidori & Spagna (2003). J. Appl. Cryst. 36, 1103]. It is devoted to the solution of crystal structures by direct and Patterson methods. Several new features implemented in SIR2004 make this program efficient: it is able to solve ab initio both small/medium-size structures as well as macromolecules (up to 2000 atoms in the asymmetric unit). In favourable circumstances, the program is also able to solve protein structures with data resolution up to 1.4–1.5 A, and to provide interpretable electron density maps. A powerful user-friendly graphical interface is provided.

SIR2002: the program

Dipartimento di Scienze della Terra Piazza UniversitaÁ, 06100 Perugia, Italy, Istituto di Cristallografia, CNR, Sezione di Monterotondo, CP 10, Monterotondo Stazione, 00016 Roma, Italy, Istituto di Cristallografia, CNR, c/o Dipartimento Geomineralogico, UniversitaÁ di Bari, Campus Universitario, Via Orabona 4, 70125 Bari, Italy, and CNR, Istituto di Cristallografia c/o Dipartimento Geomineralogico, UniversitaÁ di Bari, Campus Universitario, Via Orabona 4, 70125 Bari, Italy. Correspondence e-mail: carmelo.giacovazzo@ic.cnr.it

IL MILIONE: a suite of computer programs for crystal structure solution of proteins

IL MILIONEIl Milione is the title of the book by Marco Polo, dictated to Rustichello da Pisa in 1298 in the Genova prison where Marco was imprisoned after a naval battle between Genova and Venezia. Il Milione is a travel report: the name suggests the millions of marvels seen during the travel. Most contemporaries thought that they were a million tales. Our program is also a travel report, but in the world of crystallography. is a suite of computer programs devoted to protein crystal structure determination by X-ray crystallography. It may be used in the following key activities. (a) Ab initio phasing, via Patterson or direct methods. The program may succeed even with structures with up to 6000 non-H atoms in the asymmetric unit, provided that atomic resolution is available, and with data at quasi-atomic resolution (1.4–1.5 A). (b) Single or multiple isomorphous replacement, single- or multiple-wavelength anomalous diffraction, and single or multiple isomorphous replacement with anomalous scattering techniques. In the first step the program finds the heavy-atom/anomalous scatterer substructure, then automatically uses the above information to phase protein reflections. Phase extension and refinement are performed by electron density modification techniques. (c) Molecular replacement. The orientation and the location of the protein molecules are found via reciprocal space methods. Phase extension and refinement are performed by electron density modification techniques. All the programs integrated into IL MILIONE are controlled by means of a user-friendly graphical user interface, which is used to input data and to monitor intermediate and final results by means of real-time updated messages, diagrams and histograms.

SIR2011: a new package for crystal structure determination and refinement

SIR2011, the successor of SIR2004, is the latest program of the SIR suite. It can solve ab initio crystal structures of small- and medium-size molecules, as well as protein structures, using X-ray or electron diffraction data. With respect to the predecessor the program has several new abilities: e.g. a new phasing method (VLD) has been implemented, it is able to exploit prior knowledge of the molecular geometry via simulated annealing techniques, it can use molecular replacement methods for solving proteins, it includes new tools like free lunch and new approaches for electron diffraction data, and it visualizes three-dimensional electron density maps. The graphical interface has been further improved and allows the straightforward use of the program even in difficult cases.

EXPO: a program for full powder pattern decomposition and crystal structure solution

EXPO is the integration of two programs, EXTRA and SIRPOW.92, the first devoted to full powder pattern decomposition and the second to the solution and refinement of crystal structures. The program is able to exploit the prior information obtained during the crystal structure solution process for improving the classical decomposition. EXPO also allows preliminary cycles of Rietveld refinement.

Crystal structure determination and refinement via SIR2014

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 Difference) 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.

Automated determination of the extinction symbol via electron diffraction data

The identification of the extinction symbol is routine for single-crystal X-ray data. Because of peak overlap and possible preferred orientation the task is more difficult for powder diffraction data, but recent computer programs based on probabilistic approaches have made it more automatic. This paper describes a new algorithm for the automatic identification of the Laue group and of the extinction symbol from electron diffraction intensities. The algorithm has a statistical basis and tries to deal with the severe problems arising from the often nonkinematical nature of the diffraction intensities and from the limited accuracy of the lattice parameters determined via electron diffraction. The approach has been checked using a wide set of test structures.

SIR2000, a program for the automatic ab initio crystal structure solution of proteins

A new phasing procedure is described working both in direct and in reciprocal space. The procedure has been implemented into the program SIR2000, the heir to SIR99, and it is able routinely to solve ab initio crystal structures of proteins without any use of prior information and any user intervention. The moduli and the flow diagram of SIR2000 are also described and its efficiency tested on several protein diffraction data sets. Success has been attained for crystal structures with up to almost 2000 non-hydrogen atoms in the asymmetric unit and resolution higher than 1.2 A. The phasing process is analysed to provide a better insight into the role of the various steps of the procedure.

Ab initio phasing of proteins with heavy atoms at non-atomic resolution: pushing the size limit of solvable structures up to 7890 non-H atoms in the asymmetric unit

The success of the ab initio phasing process mainly depends on two parameters: data resolution and structural complexity. In agreement with the Sheldrick rule, the presence of heavy atoms can also play a nonnegligible role in the success of direct methods. The increased efficiency of the Patterson methods and the advent of new phasing techniques based on extrapolated reflections have changed the state of the art. In particular, it is not clear how much the resolution limit and the structural complexity may be pushed in the presence of heavy atoms. In this paper, it is shown that the limits fixed by the Sheldrick rule may be relaxed if the structure contains heavy atoms and that ab initio techniques can succeed even when the data resolution is about 2 A, a limit unthinkable a few years ago. The method is successful in solving a structure with 7890 non-H atoms in the asymmetric unit at a resolution of 1.65 A, a considerable advance on the previous record of 6319 atoms at atomic resolution.

Phasing at resolution higher than the experimental resolution.

Limited experimental resolution is a unavoidable feature in macromolecular crystallography: it may hinder or make difficult the determination of the crystal structure. A novel procedure is presented which from an approximate electron-density map extrapolates the moduli and phases of non-measured reflections beyond and behind the experimental resolution limit. Applications to a set of test structures show that the extrapolation can be successfully accomplished. As a consequence, the phase estimates of the observed reflections are subsequently improved and the interpretability of the corresponding electron-density map increases. The use of the extrapolated values for the non-measured reflections provides additional information for the map, which shows a resolution higher than the experimental resolution.