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Cryo-EM Structure of K63R Ubiquitin Mutant Ribosome under Oxidative Stress
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6GQ1
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 22.45 f_angle_d 0.7781 f_chiral_restr 0.0384 f_bond_d 0.0093 f_plane_restr 0.0044
Sample K63 ubiquitinated Ribosome
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument LEICA EM GP Cryogen Name ETHANE Sample Vitrification Details
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 9629 Reported Resolution (Å) 4.2 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 (6GQ1) Refinement Space REAL Refinement Protocol FLEXIBLE FIT Refinement Target correlation coefficient Overall B Value Fitting Procedure Details
Data Acquisition Detector Type GATAN K3 (6k x 4k) Electron Dose (electrons/Å**2) 60
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) Maximum Defocus (nm) Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS Imaging Mode BRIGHT FIELD Specimen Holder Model FEI TITAN KRIOS AUTOGRID HOLDER Nominal Magnification Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version IMAGE ACQUISITION Latitude CTF CORRECTION CTFFIND ctffind4.0 MODEL FITTING UCSF Chimera chimeraX INITIAL EULER ASSIGNMENT cryoSPARC 2.12.0 FINAL EULER ASSIGNMENT RELION 3.0 CLASSIFICATION RELION 3.0 RECONSTRUCTION RELION 3.0 MODEL REFINEMENT PHENIX 1.16-3549-000
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION