Improved ligand geometries in crystallographic refinement usingAFITTinPHENIX

Abstract

Modern crystal structure refinement programs rely on geometry restraints to overcome the challenge of a low data-to-parameter ratio. While the classical Engh and Huber restraints work well for standard amino-acid residues, the chemical complexity of small-molecule ligands presents a particular challenge. Most current approaches either limit ligand restraints to those that can be readily described in the Crystallographic Information File (CIF) format, thus sacrificing chemical flexibility and energetic accuracy, or they employ protocols that substantially lengthen the refinement time, potentially hindering rapid automated refinement workflows. PHENIX-AFITT refinement uses a full molecular-mechanics force field for user-selected small-molecule ligands during refinement, eliminating the potentially difficult problem of finding or generating high-quality geometry restraints. It is fully integrated with a standard refinement protocol and requires practically no additional steps from the user, making it ideal for high-throughput workflows. PHENIX-AFITT refinements also handle multiple ligands in a single model, alternate conformations and covalently bound ligands. Here, the results of combining AFITT and the PHENIX software suite on a data set of 189 protein-ligand PDB structures are presented. Refinements using PHENIX-AFITT significantly reduce ligand conformational energy and lead to improved geometries without detriment to the fit to the experimental data. For the data presented, PHENIX-AFITT refinements result in more chemically accurate models for small-molecule ligands.

qFit-ligand reveals widespread conformational heterogeneity of drug-like molecules in X-ray electron density maps

“…Rather, we advocate including energy restraints in refinement. 52 Other conformational search methods with force fields, such as Schrodinger's ConfGen 53 and MacroModel, 54 OpenEye's Omega, 55 MOE, 56 and many other freely available tools 57 could independently validate results in the absence of data.…”

Target Identification and Mode of Action of Four Chemically Divergent Drugs against Ebolavirus Infection

“…Each structure was initially phased with rigid-body refinement using the apo GP structure (PDB ID 5JQ3) by omitting residues 190–195 of GP1 and water molecules. The subsequent structure refinement used REFMAC5 40 or PHENIX, 41 and models were rebuilt with COOT. 42 All four models were refined to reasonable R-factors with good stereochemistry.…”

Validation of ligands in macromolecular structures determined by X-ray crystallography

“…It can be noted that novel CSD structures could be expected to have RMSZ values for bonds and angles around one, and that values lower than this are not 'better'. This is particularly important in the fair treatment of structures refined with ligand restraints derived from highlevel quantum-chemical procedures (Moriarty et al, 2009), using a force field (Bell et al, 2012;Janowski et al, 2016) or through the direct use of quantum-chemical methods (Borbulevych et al, 2014;Smart et al, 2016) to represent the ligands. We conclude that Mogul bond-length and bond-angle RMSZ values are not sufficient as ligand-geometry quality metrics and hence cannot be used to assess whether the quality of ligands in the PDB is improving.…”