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. 21.1, p. 503   | 1 | 2 |

Section 21.1.7.2.6. Solvent molecules

G. J. Kleywegta*

aDepartment of Cell and Molecular Biology, Uppsala University, Biomedical Centre, Box 596, SE-751 24 Uppsala, Sweden
Correspondence e-mail: gerard@xray.bmc.uu.se

21.1.7.2.6. Solvent molecules

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Solvent molecules provide an excellent means of `absorbing' problems in both the experimental data and the atomic model. Neither their position nor their temperature factor are usually restrained (other than by the data and restraints that prevent close contacts) and sometimes even their occupancy is refined. At a resolution of ∼2 Å, crystallographers tend to model roughly one water molecule for every amino-acid residue and at 1.0 Å resolution this number increases to ∼1.6 (Carugo & Bordo, 1999[link]). When waters are placed, it should be ascertained that they can actually form hydrogen bonds, be it to protein atoms or to other water molecules. Considering that several ions that are isoelectronic with water (Na+, [\hbox{NH}_4^+]) are often used in crystallization solutions, one should keep in mind the possibility that some entities that have been modelled as water molecules could be something else (Kleywegt & Jones, 1997[link]). A method to check if water molecules could actually be sodium ions, based on the surrounding atoms, has been published (Nayal & Di Cera, 1996[link]).

References

First citation Carugo, O. & Bordo, D. (1999). How many water molecules can be detected by protein crystallography? Acta Cryst. D55, 479–483.Google Scholar
First citation Kleywegt, G. J. & Jones, T. A. (1997). Model-building and refinement practice. Methods Enzymol. 277, 208–230.Google Scholar
First citation Nayal, M. & Di Cera, E. (1996). Valence screening of water in protein crystals reveals potential Na+ binding sites. J. Mol. Biol. 256, 228–234.Google Scholar








































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