8TNQ | pdb_00008tnq

Cryo-EM structure of DDB1dB:CRBN:PT-179:SD40, conformation 1

ELECTRON MICROSCOPY

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Starting Model(s)

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

Refinement

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	4.1904
f_angle_d	0.5006
f_chiral_restr	0.0437
f_plane_restr	0.0053
f_bond_d	0.0042

Sample
Ternary Complex of DDB1dB:CRBN:PT-179 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 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	289691
Reported Resolution (Å)	2.41
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	POINT
Point Symmetry	C1

Map-Model Fitting and Refinement
Id	1 (8G46, 5FQD, 6H0F)
Refinement Space	REAL
Refinement Protocol	OTHER
Refinement Target	Cross-correlation coefficient
Overall B Value	70
Fitting Procedure
Details	Phenix real-space refinement without rigid body, with ADP.

Data Acquisition
Detector Type	GATAN K3 BIOQUANTUM (6k x 4k)
Electron Dose (electrons/Å**2)	52

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	TFS KRIOS
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	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	4.2.0
MODEL FITTING	UCSF ChimeraX	1.6.1
MODEL REFINEMENT	PHENIX	1.20.1
INITIAL EULER ASSIGNMENT	cryoSPARC	4.2.0
FINAL EULER ASSIGNMENT	cryoSPARC	4.2.0
CLASSIFICATION	RELION	4.0.1
RECONSTRUCTION	cryoSPARC	4.2.0

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION		6798113