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Fusidic acid-locked Escherichia coli 70S ribosome with Staphylococcus aureus EF-G and a tRNA in pe/E chimeric state (CHI)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8P2H
Refinement RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 10.686 r_dihedral_angle_6_deg 6.535 r_dihedral_angle_2_deg 6.001 r_lrange_it 5.238 r_lrange_other 5.238 r_dihedral_angle_1_deg 4.136 r_mcangle_it 2.51 r_mcangle_other 2.51 r_scangle_it 2.499 r_scangle_other 2.499
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 10.686 r_dihedral_angle_6_deg 6.535 r_dihedral_angle_2_deg 6.001 r_lrange_it 5.238 r_lrange_other 5.238 r_dihedral_angle_1_deg 4.136 r_mcangle_it 2.51 r_mcangle_other 2.51 r_scangle_it 2.499 r_scangle_other 2.499 r_scbond_it 1.406 r_scbond_other 1.406 r_mcbond_it 1.356 r_mcbond_other 1.356 r_angle_refined_deg 0.727 r_dihedral_angle_other_2_deg 0.727 r_angle_other_deg 0.279 r_nbtor_refined 0.221 r_symmetry_nbd_other 0.202 r_nbd_refined 0.151 r_xyhbond_nbd_refined 0.128 r_symmetry_nbtor_other 0.072 r_symmetry_xyhbond_nbd_other 0.067 r_chiral_restr 0.03 r_bond_refined_d 0.003 r_gen_planes_refined 0.003 r_gen_planes_other 0.001 r_bond_other_d
Sample Staphylococcus aureus EF-G on 70S ribosomes Sample Components Staphylococcus aureus EF-G mRNA 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 88568 Reported Resolution (Å) 2.24 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT
Map-Model Fitting and Refinement Id 1 (8P2H, 9GHE, 7N2C) Refinement Space REAL 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) 40
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 130000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION cryoSPARC 4.4.1 IMAGE ACQUISITION EPU CTF CORRECTION cryoSPARC 4.4.1 MODEL FITTING Coot 0.9.8.92 INITIAL EULER ASSIGNMENT cryoSPARC 4.4.1 FINAL EULER ASSIGNMENT cryoSPARC 4.4.1 CLASSIFICATION cryoSPARC 4.4.1 RECONSTRUCTION cryoSPARC 4.4.1 MODEL REFINEMENT Servalcat MODEL REFINEMENT Coot 0.9.8.92
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 2239537