ELECTRON MICROSCOPY

Sample

Complex of CRL4 E3 adapter-receptor pair DDB1 and CRBN bound to spirocyclic ligand

Specimen Preperation
Sample Aggregation State PARTICLE
Vitrification Instrument FEI VITROBOT MARK IV
Cryogen Name ETHANE
Sample Vitrification Details ?
3D Reconstruction
Reconstruction Method SINGLE PARTICLE
Number of Particles 195995
Reported Resolution (Å) 2.51
Resolution Method FSC 0.143 CUT-OFF
Other Details cryoSPARC non-uniform refinement was used for the final reconstruction of the consensus map, and cryoSPARC local refinement was used for the locally refined map of the thalidomide binding domain
Refinement Type
Symmetry Type POINT
Map-Model Fitting and Refinement
ID 1
Refinement Space REAL
Refinement Protocol FLEXIBLE FIT
Refinement Target ?
Overall B Value ?
Fitting Procedure ?
Details Initial fitting was done in ChimeraX, followed by flexible fitting in Coot. The model was refined with iterative rounds of building in Coot and refinement in PHENIX real space refine
Data Acquisition
Detector Type TFS FALCON 4i (4k x 4k)
Electron Dose (electrons/Å2) 50
Imaging Experiment
Date of Experiment ?
Temprature (Kelvin)
Microscope Model TFS KRIOS
Minimum Defocus (nm) 800
Maximum Defocus (nm) 1800
Minimum Tilt Angle (degrees) ?
Maximum Tilt Angle (degrees) ?
Nominal CS ?
Imaging Mode BRIGHT FIELD
Specimen Holder Model FEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification ?
Calibrated Magnification ?
Source FIELD EMISSION GUN
Acceleration Voltage (kV) 300
Imaging Details ?
Imaging Experiment
Task Software Package Version
PARTICLE SELECTION cryoSPARC 4.6.2
MODEL FITTING UCSF ChimeraX 1.9
MODEL FITTING Coot 0.9.8.95
INITIAL EULER ASSIGNMENT cryoSPARC 4.6.2
FINAL EULER ASSIGNMENT cryoSPARC 4.7
RECONSTRUCTION cryoSPARC 4.7
MODEL REFINEMENT PHENIX 1.20.1-4487
Image Processing
CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION Patch CTF
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