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Cryo-EM structure of the Escherichia coli 70S ribosome in complex with amikacin, mRNA, and A-, P-, and E-site tRNAs
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8EKC
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 14.27 f_angle_d 0.551 f_chiral_restr 0.035 f_bond_d 0.004 f_plane_restr 0.004
Sample Escherichia coli 70S ribosome in complex with amikacin, mRNA, and A-, P-, and E-site tRNAs
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument LEICA EM GP Cryogen Name ETHANE Sample Vitrification Details
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 234339 Reported Resolution (Å) 2.9 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 (8EKC) Refinement Space REAL Refinement Protocol RIGID BODY FIT Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type GATAN K3 BIOQUANTUM (6k x 4k) Electron Dose (electrons/Å**2) 40.5852
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model TFS KRIOS Minimum Defocus (nm) 700 Maximum Defocus (nm) 2000 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 105000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION cryoSPARC 4.1.2 IMAGE ACQUISITION SerialEM MASKING cryoSPARC 4.1.2 CTF CORRECTION cryoSPARC 4.1.2 MODEL FITTING UCSF Chimera 1.14 MODEL REFINEMENT PHENIX 1.19.2.4158 INITIAL EULER ASSIGNMENT cryoSPARC 4.1.2 FINAL EULER ASSIGNMENT cryoSPARC 4.1.2 CLASSIFICATION cryoSPARC 4.1.2 RECONSTRUCTION cryoSPARC 4.1.2
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION