EMRinger: side chain-directed model and map validation for 3D cryo-electron microscopy.
Advances in high-resolution cryo-electron microscopy (cryo-EM) require the development of validation metrics to independently assess map quality and model geometry. We report EMRinger, a tool that assesses the precise fitting of an atomic model into the map during refinement and shows how radiation damage alters scattering from negatively charged amino acids. EMRinger (https://github.com/fraser-lab/EMRinger) will be useful for monitoring progress in resolving and modeling high-resolution features in cryo-EM.
Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, USA.|Graduate Group in Biophysics, University of California, San Francisco, San Francisco, California, USA.
Benjamin A
http://orcid.org/0000-0002-1016-862X
BA
Barad
Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA.
Nathaniel
N
Echols
Graduate Program in Biological Physics, Structure and Design, University of Washington, Seattle, Washington, USA.|Department of Biochemistry, University of Washington, Seattle, Washington, USA.
Ray Yu-Ruei
RY
Wang
Keck Advanced Microscopy Laboratory, Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, California, USA.
Yifan
Y
Cheng
Department of Biochemistry, University of Washington, Seattle, Washington, USA.|Institute for Protein Design, Seattle, Washington, USA.
Frank
F
DiMaio
Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA.|Department of Bioengineering, University of California, Berkeley, Berkeley, California, USA.
Paul D
PD
Adams
Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, USA.
James S
http://orcid.org/0000-0002-5080-2859
JS
Fraser
D020285:Cryoelectron Microscopy / Q000379:methods*; D018360:Crystallography, X-Ray; D030562:Databases, Protein; D007091:Image Processing, Computer-Assisted / Q000379:methods*; D008958:Models, Molecular; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D015203:Reproducibility of Results; D012984:Software; D050916:TRPV Cation Channels / Q000737:chemistry
D011506:Proteins; D050916:TRPV Cation Channels; C493922:Trpv1 protein, rat