Experiment: 8TNP

Cryo-EM structure of DDB1dB:CRBN:Pomalidomide:SD40

ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5FQD
experimental model	PDB	8G46
experimental model	PDB	6H0F

Refinement

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	4.8878
f_angle_d	0.5479
f_chiral_restr	0.045
f_bond_d	0.0045
f_plane_restr	0.0038

Sample
Ternary Complex of DDB1dB:CRBN:pomalidomide with SD40

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	LEICA EM GP
Cryogen Name	ETHANE
Sample Vitrification Details	Leica EM-GP plunge freezer with chamber conditions of 10 C and 90% relative humidity. Grids were first pre-incubated with 4 uL of 10 uM CRBN-agnostic ...	Leica EM-GP plunge freezer with chamber conditions of 10 C and 90% relative humidity. Grids were first pre-incubated with 4 uL of 10 uM CRBN-agnostic IKZF1_140-196_Q146A,G151N for 1 minute and then blotted from behind for 4 s. Immediately, 4 uL of mixture 1 diluted 10-fold--with the dilution buffer during the 1-minute incubation time--was applied to the grids before blotting for 4 s and plunging into liquid ethane at -181 C.

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	55205
Reported Resolution (Å)	3.3
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	POINT
Point Symmetry	C1

Map-Model Fitting and Refinement
Id	1 (5FQD, 8G46, 6H0F)
Refinement Space	REAL
Refinement Protocol	OTHER
Refinement Target	CC
Overall B Value	102
Fitting Procedure
Details	Phenix real-space refinement without rigid body

Data Acquisition
Detector Type	GATAN K3 (6k x 4k)
Electron Dose (electrons/Å**2)	53.8

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	TFS TALOS
Minimum Defocus (nm)	800
Maximum Defocus (nm)	2000
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	36000
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	200
Imaging Details

EM Software
Task	Software Package	Version
PARTICLE SELECTION	Topaz	0.2.5
IMAGE ACQUISITION	SerialEM	4.1b
CTF CORRECTION	cryoSPARC	4.2.0
MODEL FITTING	UCSF ChimeraX	1.5
INITIAL EULER ASSIGNMENT	cryoSPARC	4.2.0
FINAL EULER ASSIGNMENT	cryoSPARC	4.2.0
CLASSIFICATION	cryoSPARC	4.2.0
RECONSTRUCTION	cryoSPARC	4.2.0
MODEL REFINEMENT	PHENIX	1.19.2

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION		1254659