Aug 1, 2015

RNA Structure Refinement Using the ERRASER-Phenix Pipeline

Methods in Molecular Biology
Fang-Chieh ChouRhiju Das

Abstract

The final step of RNA crystallography involves the fitting of coordinates into electron density maps. The large number of backbone atoms in RNA presents a difficult 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 refinement in Phenix with the Rosetta-based real-space refinement protocol ERRASER (Enumerative Real-Space Refinement ASsisted by Electron density under Rosetta). The combination of ERRASER and Phenix can improve the geometrical quality of RNA crystallographic models while maintaining or improving the fit 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, and via an application in the Rosetta On-line Server that Includes Everyone (ROSIE).

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Mentioned in this Paper

Computer Software
Asphondylia rosetta
Atom (substance)
Fast Electrons
Electron Density
Crystallography, X-Ray
Bw protein, Drosophila
Computer Programs and Programming
Pyrimidine
Structure

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