9EGK | pdb_00009egk

E3 ubiquitin ligase HUWE1 homolog Tom1p in closed-conformation with internal Acidic Domain deletion

ELECTRON MICROSCOPY

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Refinement

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	4.945
f_angle_d	0.601
f_chiral_restr	0.055
f_plane_restr	0.005
f_bond_d	0.004

Sample
Yeast E3 ubiquitin ligase Tom1p with an internal truncation at the acidic domain (residues 1873-2131).

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	FEI VITROBOT MARK I
Cryogen Name	ETHANE
Sample Vitrification Details	Specimens were prepared on Quantifoil R 2/2 Cu300 grids after glow discharge for 1 minute at 25 mA. The detergent sample was concentrated to 8.1 mg/mL in 0.01% CHAPS and 0.05% NP-40. 2.5 uL of sample was applied to grids and blotted for 2.5 seconds before vitrification by plunging into liquid ethane. For samples without detergent, protein was concentrated to 0.44 mg/mL and blotted for 1.5 seconds before vitrification.

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	462711
Reported Resolution (Å)	3.07
Resolution Method	FSC 0.143 CUT-OFF
Other Details	The separately processed dataset #1 and #2 particles were combined for a total of 531,549 starting particles for further processing and refinement. A round of 2D classification resulted in selection of 477,889 particles, which were Fourier cropped from a box size of 680 to 320 pixels for further processing. Two-component 3DVA was performed after map refinement of the combined dataset with a filter resolution of 4 A. 3DVA display was subsequently run to give 8 intermediates along the first principal component at a filter resolution of 5 A. The top 4 intermediates with the highest number of particles were combined to yield 462,711 and refined using non-uniform refinement to an estimated overall resolution of 3.07 A.
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	GATAN K3 (6k x 4k)
Electron Dose (electrons/Å**2)	47

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
Imaging Mode	OTHER
Specimen Holder Model
Nominal Magnification
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details

EM Software
Task	Software Package	Version
PARTICLE SELECTION	cryoSPARC
CTF CORRECTION	cryoSPARC
MODEL REFINEMENT	PHENIX
CLASSIFICATION	cryoSPARC
RECONSTRUCTION	cryoSPARC

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
NONE