Riccardo Spagna

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.

Synthesis, characterization and antioxidant activity of new copper(I) complexes of scorpionate and water soluble phosphane ligands

New copper(I) complexes have been synthesised from the reaction of CuCl with potassium hydrotris(4-bromo-1H-pyrazol-1-yl)borate, KTp4Br or lithium bis(3,5-dimethylpyrazol-1-yl)acetate, Li[L2CO2] ligands and 4- or 2-(diphenylphosphane)benzoic acid or tris(m-sulfonatophenyl)posphine trisodium salt (TPPTS) coligands. The complexes obtained have been characterized by elemental analyses and FT-IR in the solid state, and by NMR (1H and 31P[1H]) and electrospray mass spectrometry (ESI-MS) in solution. Single crystal structural characterisation was undertaken for the [Cu[PPh2(4-C6H4COOH)](Tp4Br)] derivative, an interesting dimeric supramolecular assembly. A chemiluminescence study has demonstrated the superoxide scavenging activity of these new copper complexes. The Comet assay was used to evaluate the impairment of DNA in rat epithelial cells exposed to different reactive nitrogen species. In addition, the same complexes were included in this study to determine their efficacy as antioxidants in mitigating oxidative DNA damage. The parameter tail moment, used as an index of DNA damage, showed that the complex [Cu[PPh2(4-C6H4COOH)](Tp4Br)] remarkably inhibited DNA strand breaks induced by the different nitrogen oxide species. The other copper complexes under study showed a different ability to reduce tail moment values depending on the type of RNOS donor used.

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.

Organotin(IV) polypyrazolylborates VII. Hydridotris (3,4,5-trimethyl-1 H-pyrazol-1-yl) borates. X-ray crystal structures of K(HB(3,4,5-Me3Pz)3] and [HB(3,4,5-Me3Pz)3 SnMeCl2]

Abstract Tin(IV) and organotin(IV) compounds containing hydridotris(3,4,5-trimethyl-1 H-pyrazol-1-yl)borate (L3), [RnSnCl4-n-1L3] (R=Me, n = 0–2) have been synthesised and studied by NMR (1H, 13C, 119Sn) spectroscopic techniques. The compounds are not fluxional and contain six-coordinate tin(IV) with a tridentate ligand. X-ray crystal structure of [MeSnCl2L3] is reported together with that of the parent potassium hydridotris(3,4,5-trimethyl-1 H-pyrazol-1-yl)borate, K(C18H28N6B) and comparisons are made.

SIR2000-N, a program for large and small crystal structures

The program SIR2000 [Burla et al. (2000). Acta Cryst. A56, 451–457] was designed for the ab initio solution of macromolecular crystal structures, provided that the data resolution is no lower than 1.2 A. As the phasing procedure of SIR2000 is rather time consuming, modifications have been introduced to improve its efficiency and to make it additionally suitable for small molecules (new version SIR2000-N). The role of the tangent refinement in modern phasing procedures is enlightened.

SIR99, a program for the automatic solution of small and large crystal structures

The moduli and flow diagram of the program SIR99 are described. New phasing algorithms are proposed working both in direct and in reciprocal space. Their cooperative work is able to solve the structures of both small and large molecules. In particular, small proteins can be solved ab initio without any use of prior information and any user intervention. The efficiency of the various algorithms employed by SIR99 has been tested, and the role of the tangent formula clarified. The user is also provided with some practical information concerning the computer power needed.

Crystal structure of a p-tert-butylcalix[8]arene - N-methyl-morpholine complex

Abstract p-tert-Butyl-calix[8]arene crystallizes with six molecules of N-methyl-morpholine in a triclinic lattice, space group P1 with a = 12.142(3) Å, b = 16.596(4) Å, c = 17.211(2) Å, α = 83.72(2)°, β = 80.66(2)°, γ = 69.55(2)°, Z = 1. The formation of hydrogen bonds with two molecules of N-methyl-morpholine, induces the calix[8]arene skeleton to adopt a chair-like conformation in which two 3/4-cone moieties are oriented above and below the mean molecular plane, respectively. The other four solvent molecules per unit cell simply fill the interstitial voids in a “like-tubular” solid state assembly built by p-tert-butylcalix[8]arene molecules piled along the a-axis direction.