9SFL | pdb_00009sfl

Mouse otoferlin (residues 216-1931) in the lipid-bound state (merged datasets)

ELECTRON MICROSCOPY

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	9QE2

Refinement

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	5.838
f_angle_d	0.7592
f_chiral_restr	0.0493
f_plane_restr	0.0064
f_bond_d	0.0048

Sample
Mouse otoferlin (residues 216-1931) in complex with an MSP2N2 lipid nanodisc (merged datasets)

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	FEI VITROBOT MARK IV
Cryogen Name	ETHANE-PROPANE
Sample Vitrification Details	Prior to vitrification, the sample (3 uL) 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	1170290
Reported Resolution (Å)	2.27
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	POINT
Point Symmetry	C1

Map-Model Fitting and Refinement
Id	1 (9QE2)
Refinement Space	REAL
Refinement Protocol	OTHER
Refinement Target
Overall B Value	84.15
Fitting Procedure
Details

Data Acquisition
Detector Type	FEI FALCON IV (4k x 4k)
Electron Dose (electrons/Å**2)	37.97

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	TFS KRIOS
Minimum Defocus (nm)	800
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	cryoSPARC	v.4.7
CLASSIFICATION	cryoSPARC	v.4.7
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		7049831