The Biological Macromolecule Crystallization Database: crystallization procedures and strategies

Abstract

The Biological Macromolecule Crystallization Database (BMCD) archives crystallization data from published reports for all forms of biological macromolecules that have produced crystals suitable for X-ray diffraction studies. The information includes the crystallization conditions, crystal data, comments about the crystallization procedure and information on the biological macromolecule or biological macromolecule complex. Crystallization procedures, including fast screens and more general procedures, can be developed effectively using this web-based resource (http://wwwbmcd.nist.gov:8080/bmcd/bmcd.html).

“Hot” Macromolecular Crystals

“…Crystallization conditions were screened with the Protein Complex Suite Screen. 14, 15 In the case of the TM1030:DNA complex, drops were created by mixing 1.2 μL of screen solution and 1.2 μL of a solution containing 2:1 mixture of TM1030 (protein forms dimer) and palindromic DNA in 500 mM NaCl and 10 mM HEPES pH 7.5. Identical plates were stored in incubators at 4, 20, 37 and 50° C. Tracking of crystallization experiments and analysis of the results was performed using the Xtaldb crystallization expert system 16.…”

“…The Biological Macromolecular Crystallization Database (BMCD) contains manually curated crystallization parameters for a set of crystal structures, using information derived both from the PDB and from structure citations in the published literature. 14 BMCD revision 4.02, which contains information on 14372 crystal entries, was queried through its web interface (http://xpdb.nist.gov:8060/BMCD4/) and the reported T c for each structure was extracted. The values of T c in MYPDB and the BMCD for the structures that report crystal unit cell parameters (e,g, those solved by X-ray or neutron diffraction) were used to calculate the distribution by year Fig.…”

Which strategy for a protein crystallization project?

“…The chemical composition space for crystallization is enormous. 383 different compounds have been used in crystallizations reported in the Biological Macromolecular Crystallization Database [63,64]. There are four general categories of precipitants: (i) salts, (ii) volatile organic solvents, (iii) polymers, and (iv) nonvolatile organic alcohols.…”

“…Many of the current strategies have benefited from the Biological Macromolecule Crystallization Database (http://wwwbmcd.nist. gov:8080/bmcd/bmcd.html) [64,84]. As of June 2003, the BMCD included 3547 crystal entries from 2526 biological macromolecules for which diffraction-quality crystals have been obtained.…”

▪ Introduction

“…If the lifetime of bound water is long, they lose their ability to escort surface charge movements of proteins during structural transitions. Therefore, even without a crystal lattice, proteins can be dehydrated in the high concentration salt solutions typically used in protein crystallization (Gilliland, Tung et al 2002). This is an overlooked but important effect of crystallization on protein dynamics.…”