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Cryo-EM structure of Tom1 (S. cerevisiae)
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 4.846 f_angle_d 0.423 f_chiral_restr 0.034 f_bond_d 0.003 f_plane_restr 0.003
Sample Full length structure, S. cerevisiae Tom1
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument LEICA EM GP Cryogen Name ETHANE Sample Vitrification Details CHAPSO detergent added to final conc. of 0.3 mM. Sample applied twice.
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 451216 Reported Resolution (Å) 3 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT
Map-Model Fitting and Refinement Id 1 Refinement Space Refinement Protocol Refinement Target Overall B Value 121 Fitting Procedure Details
Data Acquisition Detector Type GATAN K3 BIOQUANTUM (6k x 4k) Electron Dose (electrons/Å**2) 53.687
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model TFS KRIOS Minimum Defocus (nm) 1100 Maximum Defocus (nm) 2200 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 4.4.1 IMAGE ACQUISITION SerialEM 4.1b CTF CORRECTION cryoSPARC 4.4.1 MODEL FITTING UCSF ChimeraX 1.6.1 MODEL FITTING ISOLDE 1.6.0 MODEL REFINEMENT PHENIX 1.19.2-4158 INITIAL EULER ASSIGNMENT cryoSPARC 4.4.1 FINAL EULER ASSIGNMENT cryoSPARC 4.4.1 CLASSIFICATION cryoSPARC 4.4.1 RECONSTRUCTION cryoSPARC 4.4.1
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 4216890