An enhanced set of displacement parameter restraints in CRYSTALS

Abstract

Crystallographic restraints are widely used during refinement of small-molecule and macromolecular crystal structures. They can be especially useful for introducing additional observations and information into structure refinements against low-quality or low-resolution data (e.g. data obtained at high pressure) or to retain physically meaningful parameter values in disordered or unstable refinements. However, despite the fact that the anisotropic displacement parameters (ADPs) often constitute more than half of the total model parameters determined in a structure analysis, there are relatively few useful restraints for them, examples being Hirshfeld rigid-bond restraints, direct equivalence of parameters and SHELXL RIGU-type restraints. Conversely, geometric parameters can be subject to a multitude of restraints (e.g. absolute or relative distance, angle, planarity, chiral volume, and geometric similarity). This article presents a series of new ADP restraints implemented in CRYSTALS [Parois, Cooper & Thompson (2015), Chem. Cent. J. 9, 30] to give more control over ADPs by restraining, in a variety of ways, the directions and magnitudes of the principal axes of the ellipsoids in locally defined coordinate systems. The use of these new ADPs results in more realistic models, as well as a better user experience, through restraints that are more efficient and faster to set up. The use of these restraints is recommended to preserve physically meaningful relationships between displacement parameters in a structural model for rigid bodies, rotationally disordered groups and low-completeness data.

How anisotropic and isotropic atomic displacement parameters monitor protein covalent bonds rigidity: isotropic B-factors underestimate bond rigidity

“…Covalent bonds are highly rigid and their deformation implies severe energy costs (Slater 1968 ). This has been exploited in macromolecular crystallography with the introduction of refinement restraints (Tronrud 1996 ; Thorn et al 2012 ; Parois et al 2018 ), which essentially assume that the difference of the mean-square displacements of atoms A and Z along the covalent bond A–Z must be close to zero. These restraints are usually relaxed at very high resolution, when they are no more essential to ensure a physically and chemically realistic structure description.…”