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Cryo-EM structure of Tom1-UBE2D2-ubiquitin complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold experimental model PDB 4V3L
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 4.317 f_angle_d 0.445 f_chiral_restr 0.036 f_plane_restr 0.003 f_bond_d 0.002
Sample Ternary complex of E3 ubiquitin ligase Tom1 with E2 ubiquitin conjugating enzyme UBE2D2 and ubiquitin
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument LEICA EM GP Cryogen Name ETHANE Sample Vitrification Details CHAPSO detergent added to final conc. of 0.2 mM. Sample applied twice.
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 246341 Reported Resolution (Å) 2.8 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 (4V3L, 4V3L) Refinement Space REAL Refinement Protocol OTHER Refinement Target Cross-correlation coefficient Overall B Value 89.6 Fitting Procedure Details Phenix real-space refinement
Data Acquisition Detector Type GATAN K3 BIOQUANTUM (6k x 4k) Electron Dose (electrons/Å**2) 56.13
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model TFS KRIOS Minimum Defocus (nm) 800 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 Topaz 0.2.5 IMAGE ACQUISITION SerialEM 4.1b CTF CORRECTION cryoSPARC 4.4.1 MODEL FITTING UCSF ChimeraX 1.6.1 MODEL FITTING ISOLDE 1.6.0 INITIAL EULER ASSIGNMENT cryoSPARC 4.4.1 FINAL EULER ASSIGNMENT cryoSPARC 4.4.1 CLASSIFICATION cryoSPARC 4.4.1 RECONSTRUCTION cryoSPARC 4.4.1 MODEL REFINEMENT PHENIX 1.19.2-4158
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 11388836 Initial 2D classes assisted template picking in cryoSPARC Live.