Experiment: 8QH5

CryoEM structure of UVSSA(VHS)-CSA-DDB1-DDA1

ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7OO3
experimental model	PDB	6ZX9
experimental model	PDB	6UD7
in silico model	AlphaFold	Q2YD98

Sample
Ternary complex of UVSSA(VHS)-CSA-DDB1-DDA1

Specimen Preparation
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	294142
Reported Resolution (Å)	3.4
Resolution Method	FSC 0.143 CUT-OFF
Other Details	Combined from focused maps reconstructed with various particle numbers.
Refinement Type
Symmetry Type	POINT
Point Symmetry	C1

Map-Model Fitting and Refinement
Id	1 (7OO3, 7OO3, 6ZX9, 6UD7)
Refinement Space	REAL
Refinement Protocol	RIGID BODY FIT
Refinement Target
Overall B Value
Fitting Procedure
Details	Additional densities are observed near several cysteine residues (A/Cys222, A/Cys260, A/Cys288, B/Cys363, B/Cys725, B/Cys1008). We expect these are ox ...	Additional densities are observed near several cysteine residues (A/Cys222, A/Cys260, A/Cys288, B/Cys363, B/Cys725, B/Cys1008). We expect these are oxidized products or crosslinking side products.

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

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	FEI TITAN KRIOS
Minimum Defocus (nm)	1000
Maximum Defocus (nm)	3000
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	81000
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details	Collected on Krios 1 at Netherlands Center for Electron Nanoscopy (NeCEN)

EM Software
Task	Software Package	Version
PARTICLE SELECTION	Topaz
CTF CORRECTION	cryoSPARC
CTF CORRECTION	RELION
MODEL FITTING	UCSF Chimera
MODEL FITTING	PHENIX
MODEL FITTING	Coot
MODEL REFINEMENT	PHENIX
INITIAL EULER ASSIGNMENT	cryoSPARC
INITIAL EULER ASSIGNMENT	RELION	3.1.3
FINAL EULER ASSIGNMENT	RELION	3.1.3
RECONSTRUCTION	RELION	3.3.3

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION		723908