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E. coli 70S ribosome, conformational ground state mutation in SSU-h41, with A/P- and P/E-site tRNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7K00
Refinement RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 9.764 r_dihedral_angle_6_deg 9.46 r_dihedral_angle_1_deg 5.322 r_lrange_it 4.663 r_lrange_other 4.663 r_dihedral_angle_2_deg 3.212 r_mcangle_it 3.081 r_mcangle_other 3.081 r_scangle_it 2.507 r_scangle_other 2.507
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 9.764 r_dihedral_angle_6_deg 9.46 r_dihedral_angle_1_deg 5.322 r_lrange_it 4.663 r_lrange_other 4.663 r_dihedral_angle_2_deg 3.212 r_mcangle_it 3.081 r_mcangle_other 3.081 r_scangle_it 2.507 r_scangle_other 2.507 r_mcbond_it 1.697 r_mcbond_other 1.696 r_scbond_it 1.414 r_scbond_other 1.414 r_angle_refined_deg 0.714 r_dihedral_angle_other_2_deg 0.415 r_angle_other_deg 0.268 r_nbtor_refined 0.222 r_symmetry_nbd_other 0.177 r_nbd_refined 0.142 r_xyhbond_nbd_refined 0.114 r_symmetry_nbtor_other 0.074 r_chiral_restr 0.028 r_symmetry_xyhbond_nbd_other 0.022 r_metal_ion_refined 0.016 r_bond_refined_d 0.004 r_gen_planes_refined 0.003 r_gen_planes_other 0.001 r_bond_other_d
Sample E. coli 70S ribosome
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE Sample Vitrification Details
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 13469 Reported Resolution (Å) 2.5 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT
Map-Model Fitting and Refinement Id 1 (7K00) Refinement Space RECIPROCAL Refinement Protocol Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type GATAN K3 BIOQUANTUM (6k x 4k) Electron Dose (electrons/Å**2) 49.88
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model TFS KRIOS Minimum Defocus (nm) 300 Maximum Defocus (nm) 2000 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS 2.7 Imaging Mode BRIGHT FIELD Specimen Holder Model Nominal Magnification 165000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION cryoSPARC 4.5.1 IMAGE ACQUISITION EPU CTF CORRECTION cryoSPARC 4.5.1 MODEL FITTING UCSF ChimeraX 1.8 MODEL REFINEMENT REFMAC 5.8.0430 INITIAL EULER ASSIGNMENT cryoSPARC 4.5.1 FINAL EULER ASSIGNMENT cryoSPARC 4.6.2 CLASSIFICATION cryoSPARC 4.5.1 RECONSTRUCTION cryoSPARC 4.6.2
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION