The use of dummy atoms in X-ray macromolecular crystallography

Abstract

“Atomicity” plays an outstanding role in the current crystallographic methods of structure solution. We have been recently reminded by Sheldrick et al. (Sheldrick, G.M., Hauptman, H.A., Weeks, C.M., Miller, R. and Usón, I. (2001). Direct methods. In: Rossmann, M. and Arnold, E. (Eds.), International Tables for Crystallography, Vol. F, pp. 333–345, Kluwer Academic Publishers, Dordrecht/Boston/London), “Owing to the atomicity of crystal structures and the redundancy of the known magnitudes, the phase problem is overdetermined and is, therefore, solvable in principle”. The Introduction gives a brief overview of the traditional ways to use the concept of atomicity for the solution of the phase problem of crystallography. The main part of the review demonstrates how atomicity is used in the situations when the “atoms” introduced cannot be associated any longer with the chemical atoms; these artificial mathematical entities are called “dummy atoms”. The main goal of the review is to present the known applications of the concept of atomicity in macromolecular crystallography and especially in the solution of the phase problem. The reader can address himself to the corresponding articles for a more profound analysis of particular problems that, in view of the extremely wide variety of the field, cannot be discussed here in more detail.