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

M C Burla; M Camalli; B Carrozzini; G L Cascarano; C Giacovazzo; G Polidori; R Spagna

doi:10.1107/s0108767300006966

Home/Archive/PubMed

PubMed · 10967523

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

M C Burla·M Camalli·B Carrozzini·G L Cascarano·C Giacovazzo·G Polidori·R Spagna

View original source ↗Export metadata ↓

Abstract

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.

Explore related subjects

Crystallography Enzymes Proteins Software Solutions Journal Article

Keep this discovery

Explore connections, maps & timelines

BibTeX RIS

M C Burla, M Camalli, B Carrozzini, G L Cascarano, C Giacovazzo, G Polidori, R Spagna. 2000. SIR2000, a program for the automatic ab initio crystal structure solution of proteins.. https://doi.org/10.1107/s0108767300006966

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related citations

PubMed2007

The same but different: isomorphous methods for phasing and high-throughput ligand screening.

Isomorphous difference methods allow rapid and detailed visualization of localized changes in macromolecular structures, whether as a result of mutation or the binding of ligands. Practical aspects of isomorphous methods and differential crystallography are presented, particularly in their application to the phasing of new structures by multiple isomorphous replacement and the detection and characterization of ligand binding. Techniques for maintaining isomorphism between crystals to maximize the differential signal are covered, as are the computational steps involved in generating difference electron density maps. Frontier applications such as determining single-site ligand-binding affinities crystallographically, high-throughput screening of combinatorial compound libraries, in crystallo competition assays, and inferring protein function via exogenous ligand-binding screens are discussed.

Crystallography↗

PubMed2007

Crystallographic software: a sustainable resource for the community.

Virtually all software is constantly changing and evolving (and crystallographic software is no exception), which makes it nearly impossible to write a chapter that will remain current. In this chapter, we introduce CRYSTAL, a website (http://crystal.uvm.edu) where a comprehensive list of available crystallographic packages for each step of macromolecular structure determination will be maintained. Additionally, we provide links to books, journals, and a number of educational sites on crystallography. For each program/site included at CRYSTAL, a detailed description will include: the most current version, the authors, and appropriate operating systems to host the program. Links to download the programs, available tutorials, and references to cite when using the program/site are also provided.

Crystallography↗

PubMed2006

Architecture of fiber network: from understanding to engineering of molecular gels.

A new approach of engineering of molecular gels was established on the basis of a nucleation-initiated network formation mechanism. A variety of gel network structures can be obtained by regulating the starting temperature of the sol-gel transition. This enables us to tune the network from the spherulitic domains pattern to the extensively interconnected fibrillar network. As the consequence of fibrous network structure turning, desirable rheological and other in-use properties of the materials can be obtained accordingly. This approach of micro-/nanostructural fabrication may open up a new route for micro-/nanofunctional materials engineering in general.

Crystallography↗