RNA structure refi nement using the erraser-phenix pipeline

Abstract

The fi nal step of RNA crystallography involves the fi tting of coordinates into electron density maps. The large number of backbone atoms in RNA presents a diffi cult and tedious challenge, particularly when experimental density is poor. The ERRASER-Phenix pipeline can improve an initial set of RNA coordinates automatically based on a physically realistic model of atomic-level RNA interactions. The pipeline couples diffraction-based refi nement in Phenix with the Rosetta-based real-space refi nement protocol ERRASER ( E numerative R eal-Space R efi nement AS sisted by E lectron density under R osetta). The combination of ERRASER and Phenix can improve the geometrical quality of RNA crystallographic models while maintaining or improving the fi t to the diffraction data (as measured by R free). Here we present a,complete tutorial for running ERRASER-Phenix through the Phenix GUI, from the command-line, via an application in the Rosetta On-line Server that Includes Everyone (ROSIE).