Improved ligand geometries in crystallographic refinement using AFITT in PHENIX

Area of Science:

• Crystallography
• Structural Biology
• Computational Chemistry

Background:

• Crystal structure refinement programs often use geometry restraints to manage low data-to-parameter ratios.
• Standard restraints are effective for amino acids but struggle with the chemical complexity of small-molecule ligands.
• Current methods for ligand restraints either limit chemical flexibility or increase refinement time, hindering automated workflows.

Purpose of the Study:

• To introduce PHENIX-AFITT, a refinement method that integrates molecular mechanics force fields for small-molecule ligands.
• To evaluate the effectiveness of PHENIX-AFITT in improving ligand geometry and chemical accuracy in protein-ligand complexes.
• To assess the impact of PHENIX-AFITT on refinement time and data fit.

Main Methods:

• Utilized the PHENIX software suite combined with the AFITT refinement protocol.
• Applied PHENIX-AFITT to a dataset of 189 protein-ligand structures from the Protein Data Bank (PDB).
• Integrated full molecular-mechanics force fields directly into the refinement process for selected ligands.

Main Results:

• Refinements using PHENIX-AFITT significantly reduced the conformational energy of small-molecule ligands.
• Improved ligand geometries were observed without negatively impacting the fit to experimental diffraction data.
• The method demonstrated capability in handling multiple ligands, alternate conformations, and covalently bound ligands within a single model.

Conclusions:

• PHENIX-AFITT provides a chemically accurate and energetically favorable refinement for small-molecule ligands in crystallography.
• The integration of molecular mechanics force fields streamlines the restraint generation process, ideal for high-throughput studies.
• This approach enhances structural models by improving ligand quality while maintaining compatibility with standard refinement protocols.