9GIK | pdb_00009gik

Full-lenght Nedd4-2 E3 ubiquitin ligase

ELECTRON MICROSCOPY

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2ONI
experimental model	PDB	2NSQ

Refinement

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	8.739
f_angle_d	0.413
f_chiral_restr	0.038
f_plane_restr	0.003
f_bond_d	0.002

Sample
Nedd4-2

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument
Cryogen Name	ETHANE
Sample Vitrification Details

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	225759
Reported Resolution (Å)	3.58
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	POINT

Map-Model Fitting and Refinement
Id	1 (2ONI, 2NSQ)
Refinement Space	REAL
Refinement Protocol
Refinement Target
Overall B Value
Fitting Procedure
Details

Data Acquisition
Detector Type	GATAN K3 BIOQUANTUM (6k x 4k)
Electron Dose (electrons/Å**2)	40

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	FEI TITAN KRIOS
Minimum Defocus (nm)	700
Maximum Defocus (nm)	2800
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
Imaging Mode	BRIGHT FIELD
Specimen Holder Model
Nominal Magnification
Calibrated Magnification	105000
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details

EM Software
Task	Software Package	Version
MODEL FITTING	Coot	0.9.8
INITIAL EULER ASSIGNMENT	cryoSPARC	4.4.1
FINAL EULER ASSIGNMENT	cryoSPARC	4.4.1
CLASSIFICATION	cryoSPARC	4.4.1.
RECONSTRUCTION	cryoSPARC	4.4.1.
MODEL REFINEMENT	PHENIX	1.19.1

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