title: A simple procedure to evaluate the efficiency of bio-macromolecular rigid-body refinement by small-angle scattering.
abstract: A simple and rapid procedure is presented that enables evaluation and visualization of refinement efficiency for bio-macromolecular complexes consisting of two subunits in a given orientation by using small-angle scattering. Subunit orientations within a complex can be provided in practice by NMR residual dipolar couplings, an approach that has been combined with increasing success to complement small-angle data. The procedure is illustrated by applying it to several systems composed of two simple geometric bodies (ellipsoids) and to protein complexes from the protein data bank that vary in subunit size and anisometry. The effects of the experimental small-angle scattering range (Q-range) and data noise level on the refinement efficiency are investigated and discussed. The procedure can be used in two ways: (1) either as a quick preliminary test to probe the refinement capacity expected for a given bio-macromolecular complex prior to sophisticated and time-consuming experiments and data analysis, or (2) as an a posteriori check of the stability and accuracy of a refined model and for illustration of the residual degrees of freedom of the subunit positions that are in agreement with both small-angle data and restraints on subunit orientation (as provided, e.g., by NMR).
authors.affiliation: Extremophiles and Large Molecular Assemblies Group, Institut de Biologie Structurale Jean-Pierre Ebel, 41 rue Jules Horowitz, Grenoble, France. frank.gabel@ibs.fr
authors.forename: Frank
authors.initials: F
authors.lastname: Gabel
mesh_terms: D030562:Databases, Protein; D008958:Models, Molecular; D017434:Protein Structure, Tertiary; D021122:Protein Subunits / Q000737:chemistry; D011506:Proteins / Q000737:chemistry*; D053838:Scattering, Small Angle; D014961:X-Ray Diffraction
chemical_list: D021122:Protein Subunits; D011506:Proteins