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E. coli 70S ribosome, conformational excited 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 9.678 r_dihedral_angle_6_deg 9.507 r_lrange_it 6.646 r_lrange_other 6.646 r_dihedral_angle_1_deg 5.312 r_mcangle_it 4.653 r_mcangle_other 4.653 r_scangle_it 3.908 r_scangle_other 3.908 r_dihedral_angle_2_deg 3.207
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 9.678 r_dihedral_angle_6_deg 9.507 r_lrange_it 6.646 r_lrange_other 6.646 r_dihedral_angle_1_deg 5.312 r_mcangle_it 4.653 r_mcangle_other 4.653 r_scangle_it 3.908 r_scangle_other 3.908 r_dihedral_angle_2_deg 3.207 r_mcbond_it 2.599 r_mcbond_other 2.599 r_scbond_it 2.224 r_scbond_other 2.224 r_angle_refined_deg 0.743 r_dihedral_angle_other_2_deg 0.438 r_angle_other_deg 0.272 r_nbtor_refined 0.222 r_symmetry_nbd_other 0.177 r_nbd_refined 0.143 r_xyhbond_nbd_refined 0.125 r_symmetry_nbtor_other 0.074 r_symmetry_xyhbond_nbd_other 0.049 r_metal_ion_refined 0.045 r_chiral_restr 0.029 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 14786 Reported Resolution (Å) 2.48 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