XtalBase

http://www.xtalbase.net

Introduction

The procedures used to solve a structure by means of x-ray crystallography are constantly optimized and rationalized. Not at least this development has lead to the introduction of robots, which are capable of setting crystallization experiments merely based on the input of a set of crystallization conditions. Whereas there are effective ways of setting up crystallization trials, the design of experiments seems still be based on only a limited amount of data, which has not been collected systematically. An important aspect of crystallization of biological macromolecules is the intelligent use of prior experimental experience. Many crystallography laboratories rely on commercially available screening kits and on the quality of the selected conditions. However, these kits were developed based on only a comparatively small number of experiments. Despite the very large number of crystallization experiments, which are being performed in the course of structural genomics initiatives there is with one exception until today no comprehensive publicly available database of crystallization conditions, which could be systematically used to evaluate crystallization probabilities. The exception is the "Biological Macromolecule Crystallization Database" (BMCD). ^{1; 2} The BMCD comprises crystallization conditions, which were collected from literature.

In order to be able to handle a large body of experiment variables, to vary parameters in an automated fashion and to make it possible to use the accumulated experience in an effective way I have developed the database system XtalBase that supports the experimenter in designing, setting up, monitoring, and evaluating crystallization experiments. ³ This program hosts a crystallization database, which includes both conditions and their respective outcome in a system-wide compatible format. It is possible to use experience from all conditions registered in the system. The system includes simple and automated procedures that allow the experimenter to design new experiments based on prior knowledge. It includes a database of compounds containing information on properties, which are useful for setting up experiments such as the molecular weight, the density or solubility and a database of the crystallization experiments themselves. XtalBase contains a copy of all data published in the BMCD. It is possible to browse or search the databases for all stored information. Trivial calculations such as the calculation of volumes and amounts needed to prepare buffers or the design of pipetting schemes can be instantly performed. The program stores observations in form of codes, free text and pictures and allows a statistical evaluation of the results. In order to evaluate and use not only one's own results, but also data from other crystallization experiments recorded by the program it is possible to exchange data between different users in statistical form. On the client side the user manages his/her data via a web browser, which accesses the server via the Hypertext Transfer Protocol (HTTP). A database of unique compounds, which all components used in the experiments are based on, as well as compatible experiment scoring schemes ensure the unambiguous identification of components and thus allow users to exchange experimental results. Currently XtalBase can be used to store not only data related to crystallization, but all information pertinent to data collection, data reduction and refinement, as well as coordinates and publications. The program can be easily configured to store any kind of data. An extensive administrative interface allows creating new database fields or groups of fields. These fields are instantly available for entering data and can be instantly browsed and searched. A prototype of XtalBase is installed on http://www.xtalbase.net. The program is freely available and an installation package can be downloaded from the website.

References

1. Gilliland, G. L., Tung, M., Blakeslee, D. M. & Ladner, J. E. (1994). Biological Macromolecule Crystallization Database, Version 3.0: new features, data and the NASA archive for protein crystal growth data. Acta Cryst. D50, 408-13.

2. Gilliland, G. L., Tung, M. & Ladner, J. E. (2002). The Biological Macromolecule Crystallization Database: crystallization procedures and strategies. Acta Cryst. D58, 916-20.

3. Meining, W. (2006). XtalBase - A comprehensive data management system for macromolecular crystallography. J. Appl. Cryst. 39, 759-766.

4. Peat, T. S., Christopher, J. A. & Newman, J. (2005). Tapping the Protein Data Bank for crystallization information. Acta Cryst. 61, 1662-9.