XtalBase– a comprehensive data management system for macromolecular crystallography

Abstract

The rate at which successful crystallization experiments and new structures of macromolecules are reported is growing at a fast pace. It is therefore desirable to collect data systematically, handle these data effectively and evaluate the accumulated knowledge in an automated fashion in order to optimize procedures for crystallization and data evaluation. A new web-based program,XtalBase, has been developed in order to aid the crystallographer in designing, preparing, documenting and evaluating crystallization experiments.XtalBasehosts a database of physicochemical data of compounds commonly used for the crystallization of macromolecules. Experimental conditions are constructed either from existing commercial screening sets, by random, by interpolation between start and end concentrations, or as sets of individually composed drops. Recipes needed for the preparation of solutions and drops are instantly calculated and displayed. The program allows for documenting observations in the form of scores, notes and pictures. The experimental data recorded within the program as well as data imported from the Biological Macromolecule Crystallization Database (BMCD) can be used to estimate a probability of success for crystallization conditions. The program enables the user statistically to correlate conditions with observations not only from their own experiments but from all experiments documented within the system.XtalBaseprovides facilities for storing a large variety of data, such as a sample history, collection and refinement parameters, coordinates, as well as publication data. Data can be imported and exportedviacustomizable templates. The system can be configured to execute programs, which are fed by data from the database, and to extract data from the program output. The administrative interface allows the customization of all data tables and fields. All data can be searched in a unified search facility. The program presents the basis for a consistently defined database of crystallization data combined with tools to handle crystallization and crystallographic dataviaa web browser. The program home page is http://www.xtalbase.net.