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Human mitochondrial ribosome large subunit assembly intermediate with MTERF4-NSUN4, MRM2, MTG1 and the MALSU module
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5OOL
Refinement RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.223 r_dihedral_angle_3_deg 15.079 r_dihedral_angle_4_deg 12.877 r_lrange_it 12.186 r_dihedral_angle_1_deg 5.297 r_mcangle_it 3.807 r_scangle_it 3.462 r_mcbond_it 2.07 r_scbond_it 1.949 r_angle_refined_deg 0.927
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.223 r_dihedral_angle_3_deg 15.079 r_dihedral_angle_4_deg 12.877 r_lrange_it 12.186 r_dihedral_angle_1_deg 5.297 r_mcangle_it 3.807 r_scangle_it 3.462 r_mcbond_it 2.07 r_scbond_it 1.949 r_angle_refined_deg 0.927 r_nbtor_refined 0.282 r_nbd_refined 0.155 r_xyhbond_nbd_refined 0.125 r_chiral_restr 0.079 r_bond_refined_d 0.003 r_gen_planes_refined 0.003 r_gen_planes_other
Sample 55S subunit assembly intermediate
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument Cryogen Name ETHANE Sample Vitrification Details
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 48646 Reported Resolution (Å) 2.6 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT
Map-Model Fitting and Refinement Id 1 (5OOL) Refinement Space RECIPROCAL Refinement Protocol FLEXIBLE FIT Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type GATAN K3 BIOQUANTUM (6k x 4k) Electron Dose (electrons/Å**2) 48.2
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model TFS KRIOS Minimum Defocus (nm) Maximum Defocus (nm) Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS 2.7 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 MODEL FITTING Coot 0.93 INITIAL EULER ASSIGNMENT cryoSPARC 2.15 FINAL EULER ASSIGNMENT cryoSPARC RECONSTRUCTION cryoSPARC 2.15 MODEL REFINEMENT REFMAC 5.8.0267
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION