9SE5 | pdb_00009se5

Mouse otoferlin (216-1931) in the lipid-free, Ca2+-bound state, "open" conformation (class 2)

ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold

Refinement

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	6.3604
f_angle_d	0.9021
f_chiral_restr	0.0517
f_plane_restr	0.0073
f_bond_d	0.0041

Sample
Mouse otoferlin (residues 216-1931) in the lipid-free, Ca2+-bound state

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	FEI VITROBOT MARK IV
Cryogen Name	ETHANE-PROPANE
Sample Vitrification Details	After the application of ~3 uL sample (A280~0.42), the grid was blotted for 9 s with a blot force of 3, then plunged into liquid ethane/propane cooled ...	After the application of ~3 uL sample (A280~0.42), the grid was blotted for 9 s with a blot force of 3, then plunged into liquid ethane/propane cooled by liquid nitrogen.

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	91966
Reported Resolution (Å)	3.43
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	POINT
Point Symmetry	C1

Map-Model Fitting and Refinement
Id	1
Refinement Space	REAL
Refinement Protocol	AB INITIO MODEL
Refinement Target
Overall B Value	113.2
Fitting Procedure
Details

Data Acquisition
Detector Type	FEI FALCON IV (4k x 4k)
Electron Dose (electrons/Å**2)	38.13

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	TFS KRIOS
Minimum Defocus (nm)	1100
Maximum Defocus (nm)	2300
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

EM Software
Task	Software Package	Version
PARTICLE SELECTION	cryoSPARC	v.4.7
IMAGE ACQUISITION	EPU	v.3.6
CTF CORRECTION	cryoSPARC	v.4.7
MODEL FITTING	UCSF ChimeraX	v.1.8
INITIAL EULER ASSIGNMENT	cryoSPARC	v.4.7
FINAL EULER ASSIGNMENT	RELION	v.5.0
CLASSIFICATION	RELION	v.5.0
RECONSTRUCTION	RELION	v.5.0
MODEL REFINEMENT	PHENIX	1.21.2_5419

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION		5201261

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 R01GM157729.