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Structure of a native assembly intermediate of the human mitochondrial ribosome with unfolded interfacial rRNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3J9M
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 14.919 f_angle_d 1.024 f_chiral_restr 0.057 f_bond_d 0.01 f_plane_restr 0.007
Sample Mitochondrial ribosome large subunit with assembly factor
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE Sample Vitrification Details Sample incubated for 30 s prior to freezing.
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 134685 Reported Resolution (Å) 3.06 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 (3J9M) Refinement Space REAL Refinement Protocol OTHER Refinement Target Cross-correlation coefficient Overall B Value 85 Fitting Procedure Details
Data Acquisition Detector Type FEI FALCON II (4k x 4k) Electron Dose (electrons/Å**2) 1.56
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 130841 Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION RELION 2.0 IMAGE ACQUISITION EPU CTF CORRECTION Gctf 0.5 MODEL FITTING UCSF Chimera 1.11 MODEL FITTING Coot 0.8.8 MODEL REFINEMENT PHENIX 1.11.1 INITIAL EULER ASSIGNMENT RELION 2.0 FINAL EULER ASSIGNMENT RELION 2.0 CLASSIFICATION RELION 2.0 RECONSTRUCTION RELION 2.0.1
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION