6WCQ

Structure of a substrate-bound DQC ubiquitin ligase

ELECTRON MICROSCOPY

Refinement

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	11.807
f_angle_d	0.562
f_chiral_restr	0.038
f_plane_restr	0.003
f_bond_d	0.002

Sample
CUL1-SKP1-FBXL17-KEAP1 complex

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	FEI VITROBOT MARK IV
Cryogen Name	ETHANE-PROPANE
Sample Vitrification Details
Vitrification Instrument	FEI VITROBOT MARK IV
Cryogen Name	ETHANE-PROPANE
Sample Vitrification Details

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	160256
Reported Resolution (Å)	8.5
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	POINT
Point Symmetry	C1

Map-Model Fitting and Refinement
Id	1 (1LDK, 1X1X)
Refinement Space	REAL
Refinement Protocol	OTHER
Refinement Target
Overall B Value
Fitting Procedure
Details	Coordinates were fitted as rigid bodies or fragments in Chimera and subsequently geometry-optimized using PHENIX real space refinement.

Data Acquisition
Detector Type	GATAN K3 (6k x 4k)	GATAN K2 SUMMIT (4k x 4k)
Electron Dose (electrons/Å**2)	60	50

Imaging Experiment	1	2
Date of Experiment
Temperature (Kelvin)
Microscope Model	FEI TALOS ARCTICA	FEI TALOS ARCTICA
Minimum Defocus (nm)	2000	1500
Maximum Defocus (nm)	3000	3000
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS	2.7	2.7
Imaging Mode	BRIGHT FIELD	BRIGHT FIELD
Specimen Holder Model	OTHER	OTHER
Nominal Magnification
Calibrated Magnification
Source	FIELD EMISSION GUN	FIELD EMISSION GUN
Acceleration Voltage (kV)	200	200
Imaging Details

EM Software
Task	Software Package	Version
IMAGE ACQUISITION	SerialEM
CTF CORRECTION	CTFFIND	4
CTF CORRECTION	Gctf
MODEL FITTING	UCSF Chimera
IMAGE ACQUISITION	SerialEM
INITIAL EULER ASSIGNMENT	RELION	3
INITIAL EULER ASSIGNMENT	cryoSPARC
FINAL EULER ASSIGNMENT	RELION	3
RECONSTRUCTION	RELION	3
MODEL REFINEMENT	PHENIX

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION	As implemented in RELION.	824561	Total number of particles for both datasets. Selected using RELION auto-picking (Laplacian-of-Gaussian).

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.