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Related Experiment Video

Updated: Apr 6, 2026

Production, Crystallization, and Structure Determination of the IKK-binding Domain of NEMO

Production, Crystallization, and Structure Determination of the IKK-binding Domain of NEMO

Published on: December 28, 2019

RNA Structure Refinement Using the ERRASER-Phenix Pipeline.

Fang-Chieh Chou¹, Nathaniel Echols, Thomas C Terwilliger

¹Department of Biochemistry, Stanford University, 279 Campus Drive, Stanford, CA, 94305, USA.

Methods in Molecular Biology (Clifton, N.J.)

|August 1, 2015

Summary

This summary is machine-generated.

The ERRASER-Phenix pipeline automates RNA coordinate refinement in crystallography, improving model quality and data fit even with poor electron density. This tutorial covers its use via Phenix GUI, command-line, and ROSIE.

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Last Updated: Apr 6, 2026

Production, Crystallization, and Structure Determination of the IKK-binding Domain of NEMO

Production, Crystallization, and Structure Determination of the IKK-binding Domain of NEMO

Published on: December 28, 2019

Single Particle Cryo-Electron Microscopy: From Sample to Structure

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Published on: May 29, 2021

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Published on: December 1, 2020

Area of Science:

Structural Biology
Computational Biology
Biophysics

Background:

RNA crystallography requires fitting atomic coordinates into electron density maps.
The complexity of RNA's backbone atoms makes this process challenging, especially with low-resolution data.

Purpose of the Study:

To present a tutorial for the ERRASER-Phenix pipeline, an automated method for improving RNA crystallographic models.
To demonstrate the pipeline's ability to enhance geometric quality and data fit.

Main Methods:

The ERRASER-Phenix pipeline integrates Phenix (diffraction-based refinement) with ERRASER (Rosetta-based real-space refinement).
The protocol refines RNA coordinates using physically realistic atomic interaction models.

Main Results:

The combined ERRASER-Phenix approach improves the geometrical quality of RNA crystallographic models.
The pipeline maintains or enhances the fit to diffraction data, as indicated by R free values.

Conclusions:

ERRASER-Phenix offers an automated solution for challenging RNA coordinate fitting in crystallography.
Tutorials are provided for various platforms, including Phenix GUI, command-line, and the ROSIE web server.