Automating crystallographic structure solution and refinement of protein–ligand complexes

Abstract

A software system for automated protein–ligand crystallography has been implemented in the Phenix suite. This significantly reduces the manual effort required in high-throughput crystallographic studies.

Automated identification of elemental ions in macromolecular crystal structures

“…The protease thrombin is known to bind sodium natively (Di Cera et al, 1995) and has previously been used as a model system for ion identification based on valence calculations of solvent atoms (Nayal & Di Cera, 1996). We examined a set of ten ligand-bound structures (Biela et al, 2012) determined at near-atomic resolution (between 1.27 and 1.90 Å ), which we have used for testing automated ligandplacement and refinement (Echols et al, 2014), Each of these has two sodium ions modeled in the deposited structure, one internal and one bound by crystal contacts, both present at full occupancy with excellent density and coordination shells. For these tests the process was started from the original molecularreplacement search model without ligands; the structures were solved and refined automatically to within 2% of the final R free values.…”

Protein X-ray Crystallography and Drug Discovery

“…Full refinement of non-bound structures is time consuming and will produce no usable information, and should be avoided as much as possible. Automatic refinement pipelines include the phenix.ligand_pipeline [55], dimple from the CCP4 package [56], and Buster/TNT [57]. It has been suggested that up to a quarter of the ligands could remain undetected if refinement is not pushed to full completion [58].…”

Carbohydrate 3D structure validation

“…Although general automated tools for detecting ligands are available [39,40], currently the only carbohydrate-specific one is the CCP4 Sails program (J Agirre and K Cowtan, unpublished; URL: https://fg.oisin.rc-harwell.ac.uk/projects/sails). This software relies on deposited data for generating fingerprints of sugars which are then matched to the experimental map in a fast six-dimensional search, similarly to how the NAUTILUS program builds nucleic acid [41].…”