On the possibility of the observation of valence electron density for individual bonds in proteins in conventional difference maps.
In the last decade, high-resolution data have become available for macromolecular objects. Furthermore, ultrahigh-resolution diffraction data (resolution close to 0.6 A) have been collected for several protein crystals. This allows the study of fine details of the electron-density distribution such as the deformation density, i.e. the deviation of the experimentally determined electron density from the density composed of 'free' non-bonded atoms. This paper discusses the resolution and atomic temperature factors necessary to make the valence electron density visible at individual bonds in conventional difference maps for macromolecules. The study of theoretical maps calculated by quantum-chemistry methods allows estimation of these conditions; these results are confirmed by analysis of experimental maps for Leu-enkephalin and antifreeze protein RD1. A resolution limit close to 0.6 A was found to be highly important for refinement even when the maps were calculated at lower resolution. The refinement of the same models at near to 0.9 A resolution results in artificially increased values of the atomic displacement parameters and does not permit bond electron density to be visible in difference maps. To some extent, overestimation of the atomic displacement parameters may be restricted if dummy bond electrons are used in the refinement.
Afonine
Pavel V
PV
LCM3B, UMR 7036 CNRS, Université Henri Poincaré, Nancy 1, BP 239, Faculté des Sciences et Techniques, 54506 Vandoeuvre-lès-Nancy, France.
Lunin
Vladimir Y
VY
Muzet
Nicolas
N
Urzhumtsev
Alexandre
A
D000818:Animals; D021343:Antifreeze Proteins, Type III / Q000737:chemistry; D003198:Computer Simulation; D018360:Crystallography, X-Ray; D004524:Eels; D004583:Electrons; D004745:Enkephalins / Q000737:chemistry; D005583:Fourier Analysis; D008958:Models, Molecular; D015233:Models, Statistical; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D013696:Temperature
D021343:Antifreeze Proteins, Type III; D004745:Enkephalins; D011506:Proteins; C092813:RD3 protein, eel