ELECTRON MICROSCOPY

Sample

Ternary complex of E3 ubiquitin ligase Tom1 with E2 ubiquitin conjugating enzyme UBE2D2 and ubiquitin

Specimen Preperation
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
Map-Model Fitting and Refinement
ID 1
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/Å2) 56.13
Imaging Experiment
Date of Experiment ?
Temprature (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 ?
Imaging Experiment
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 ?
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