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Cryo-EM structure of human Tom70
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 4.143 f_angle_d 0.656 f_chiral_restr 0.037 f_plane_restr 0.005 f_bond_d 0.003
Sample Cryo-EM structure of human Tom70
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE Sample Vitrification Details 0.05% Chaps added immediately before vitrification
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 372624 Reported Resolution (Å) 3.57 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 Refinement Space Refinement Protocol Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type GATAN K3 BIOCONTINUUM (6k x 4k) Electron Dose (electrons/Å**2) 50
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model TFS KRIOS Minimum Defocus (nm) 800 Maximum Defocus (nm) 2400 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS 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 3.3.1 IMAGE ACQUISITION EPU 3.12 CTF CORRECTION cryoSPARC 3.3.1 INITIAL EULER ASSIGNMENT cryoSPARC 3.3.1 FINAL EULER ASSIGNMENT cryoSPARC 3.3.1 CLASSIFICATION cryoSPARC 3.3.1 RECONSTRUCTION cryoSPARC 3.3.1 RECONSTRUCTION DeepEMhancer MODEL REFINEMENT PHENIX
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 2627413