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Cryo-EM structure of the wild-type Thermus thermophilus 70S ribosome in complex with mRNA, A-site Q230-N5-methylated Release Factor 1, and P-site 2'-deoxy-A76-fMEAAAKC-peptidyl-tRNAcys at 2.13A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9MTP
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 13.129 f_angle_d 0.596 f_chiral_restr 0.036 f_plane_restr 0.005 f_bond_d 0.003
Sample Thermus thermophilus 70S ribosome in complex with mRNA, A-site Q230-N5-methylated Release Factor 1, and P-site 2'-deoxy-A76-fMEAAAKC-peptidyl-tRNAcys
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 617938 Reported Resolution (Å) 2.13 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 (9MTP) 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) 39.7153
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model TFS KRIOS Minimum Defocus (nm) 500 Maximum Defocus (nm) 1800 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 4.6.1 IMAGE ACQUISITION SerialEM MASKING cryoSPARC 4.6.1 CTF CORRECTION cryoSPARC 4.6.1 MODEL FITTING UCSF Chimera 1.17.3 MODEL REFINEMENT PHENIX 1.19.2.4158 INITIAL EULER ASSIGNMENT cryoSPARC 4.6.1 FINAL EULER ASSIGNMENT cryoSPARC 4.6.1 CLASSIFICATION cryoSPARC 4.6.1 RECONSTRUCTION cryoSPARC 4.6.1
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION