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Human mitochondrial RNase Z with tRNA-His-CCA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7ONU in silico model AlphaFold Q9BQ52
Refinement RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.353 r_long_range_B_refined 13.121 r_long_range_B_other 13.121 r_dihedral_angle_1_deg 6.758 r_scangle_other 5.125 r_mcangle_other 5.009 r_mcangle_it 5.008 r_dihedral_angle_2_deg 4.896 r_scbond_it 2.767 r_scbond_other 2.767
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.353 r_long_range_B_refined 13.121 r_long_range_B_other 13.121 r_dihedral_angle_1_deg 6.758 r_scangle_other 5.125 r_mcangle_other 5.009 r_mcangle_it 5.008 r_dihedral_angle_2_deg 4.896 r_scbond_it 2.767 r_scbond_other 2.767 r_mcbond_it 2.743 r_mcbond_other 2.742 r_angle_refined_deg 0.4 r_angle_other_deg 0.139 r_chiral_restr 0.041 r_bond_refined_d 0.017 r_gen_planes_refined 0.007 r_gen_planes_other 0.001 r_bond_other_d r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Sample RNAseZ with mt-tRNA-His Sample Components RNAseZ mt-tRNA-His
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument Cryogen Name ETHANE Sample Vitrification Details
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 4436 Reported Resolution (Å) 2.96 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT
Map-Model Fitting and Refinement Id 1 (7ONU) Refinement Space REAL 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
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model TFS KRIOS Minimum Defocus (nm) 400 Maximum Defocus (nm) 2000 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS Imaging Mode BRIGHT FIELD Specimen Holder Model Nominal Magnification Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION Warp 1.0.9 CTF CORRECTION Warp 1.0.9 MODEL FITTING Coot 0.9.8 MODEL REFINEMENT PHENIX 1.20.1-4487 INITIAL EULER ASSIGNMENT cryoSPARC 4.3.1 FINAL EULER ASSIGNMENT RELION 5.0-beta-1
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 4773315