10DW | pdb_000010dw

Structure of CRBN/DDB1dB-KAT2A-Compound4 ternary complex

ELECTRON MICROSCOPY

Refinement

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	4.774
f_angle_d	0.501
f_chiral_restr	0.043
f_plane_restr	0.004
f_bond_d	0.002

Sample
Compound 4 induced DDB1dB/CRBN, KAT2A-NTD ternary complex
Sample Components
DDB1dB/CRBN
KAT2A N-terminal domain

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	LEICA EM GP
Cryogen Name	ETHANE
Sample Vitrification Details	Grids were vitrified using a Leica EM GP plunge freezer operated at 90% humidity and 10C. Grids were first pre-incubated with 4uL of 10uM CRBN-agnosti ...	Grids were vitrified using a Leica EM GP plunge freezer operated at 90% humidity and 10C. Grids were first pre-incubated with 4uL of 10uM CRBN-agnostic IKZF1_140-196_Q146A,G151N for 1 minute and then back-blotted for 4s. Afterwards, 4uL of mixture was applied to the grids, followed by blotting for 4s and plunging into liquid ethane at -181 C.

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	613163
Reported Resolution (Å)	2.9
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	POINT

Map-Model Fitting and Refinement
Id	1
Refinement Space
Refinement Protocol
Refinement Target
Overall B Value
Fitting Procedure
Details

Data Acquisition
Detector Type	TFS FALCON 4i (4k x 4k)
Electron Dose (electrons/Å**2)	55.8

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	165000
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details	The grid was imaged at a 30-degree tilt

EM Software
Task	Software Package	Version
PARTICLE SELECTION	Topaz
MODEL REFINEMENT	PHENIX	1.21.2_5419
CTF CORRECTION	cryoSPARC
INITIAL EULER ASSIGNMENT	cryoSPARC
FINAL EULER ASSIGNMENT	cryoSPARC
RECONSTRUCTION	cryoSPARC

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