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Staphylococcus aureus 70S ribosome with p/E tRNA and RRF oriented towards the SSU (postTC-RRF-SSU)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9GHG in silico model AlphaFold
Refinement RMS Deviations Key Refinement Restraint Deviation s_dihedral_angle_6_deg 9.4934 s_dihedral_angle_3_deg 8.8434 s_dihedral_angle_1_deg 4.792 s_dihedral_angle_2_deg 1.8508 s_angle_nonh_deg 0.8734 s_nbd 0.1858 s_nbtor 0.1856 s_hbond_nbd 0.1327 s_metal_ion 0.0727 s_chiral_restr 0.0281
RMS Deviations Key Refinement Restraint Deviation s_dihedral_angle_6_deg 9.4934 s_dihedral_angle_3_deg 8.8434 s_dihedral_angle_1_deg 4.792 s_dihedral_angle_2_deg 1.8508 s_angle_nonh_deg 0.8734 s_nbd 0.1858 s_nbtor 0.1856 s_hbond_nbd 0.1327 s_metal_ion 0.0727 s_chiral_restr 0.0281 s_planes 0.0033 s_bond_nonh_d 0.0028
Sample S. aureus 70S ribosome in complex with a tRNA and ribosome recycling factor (RRF)
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 123631 Reported Resolution (Å) 2.2 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT
Map-Model Fitting and Refinement Id 1 (9GHG) Refinement Space 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) 30
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model TFS KRIOS Minimum Defocus (nm) 700 Maximum Defocus (nm) 1000 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 165000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION cryoSPARC 4.7.1-cuda12+250814 IMAGE ACQUISITION EPU CTF CORRECTION cryoSPARC 4.7.1-cuda12+250814 MODEL FITTING Coot 0.9.8.96 INITIAL EULER ASSIGNMENT cryoSPARC 4.7.1-cuda12+250814 FINAL EULER ASSIGNMENT cryoSPARC 4.7.1-cuda12+250814 CLASSIFICATION cryoSPARC 4.7.1-cuda12+250814 RECONSTRUCTION cryoSPARC 4.7.1-cuda12+250814 MODEL REFINEMENT Coot 0.9.8.96 MODEL REFINEMENT Servalcat 0.4.105
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 2556350