International
Tables for
Crystallography
Volume F
Crystallography of biological macromolecules
Edited by M. G. Rossmann and E. Arnold

International Tables for Crystallography (2006). Vol. F, ch. 12.1, p. 255   | 1 | 2 |

Section 12.1.8. Use of the heavy-atom data bank to select derivatives

D. Carvin,a S. A. Islam,b M. J. E. Sternbergb and T. L. Blundellc*

aBiomolecular Modelling Laboratory, Imperial Cancer Research Fund, 44 Lincoln's Inn Field, London WC2A 3PX, England,bInstitute of Cancer Research, 44 Lincoln's Inn Fields, London WC2A 3PX, England, and cDepartment of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, England
Correspondence e-mail:  tom@cryst.bioc.cam.ac.uk

12.1.8. Use of the heavy-atom data bank to select derivatives

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The heavy-atom data bank is probably best exploited by first investigating the most commonly used heavy-atom reagents with a view to obtaining mercury, platinum and uranyl derivatives that tend to bind at different sites. The most common reagents (Table 12.1.5.1[link]) can first be selected and tested for suitability in terms of amino-acid sequence, pH, buffer and salt. If there are many sulfhydryls, several mercurials might be exploited, or if there are several methionines, other platinum agents might be investigated. A high pH would argue against use of uranyl due to the insolubility of hydroxides; the presence of ammonium sulfate would argue for as low a pH as possible. The presence of citrate would imply changing the buffer for acetate if A-group metals, such as uranium or lanthanides, were to be used.

For each heavy-atom agent, the conditions of its previous use can be checked against the conditions of crystallization in the current study. Conversely, the database can be interrogated for reagents that have been used in similar conditions. In each case, derivatives that maximize the variety of ligands should be exploited.

The time of soak should be first set according to previous experience indicated in the database. However, the progress of heavy-atom substitution needs to be monitored by checking for change of colour, transparency or cracking. If cracking and disruption of the crystals occurs quickly, a less reactive reagent can be tried, and, conversely if substitution is insufficient, a more reactive reagent can be tried. If there are several cysteines, different derivatives can be obtained with mercurials of different size and hydrophobicity. In each circumstance, the data bank should provide useful information to assist in choosing reagents.

Please keep information about the heavy-atom binding sites and the heavy-atom structure-factor amplitudes. They should be submitted to the Protein Data Bank.








































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