Experiment: 9R13

Bovine complex I at pH 6.0 in the deactive state (consensus)

ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7QSN

Refinement

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	11.156
f_angle_d	0.547
f_chiral_restr	0.039
f_plane_restr	0.004
f_bond_d	0.002

Sample
Bovine complex I at pH 6.0 in the deactive state (consensus)

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	FEI VITROBOT MARK IV
Cryogen Name	ETHANE
Sample Vitrification Details	Blotted with a force of -10 for 10 seconds prior to plunge freezing.

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	128687
Reported Resolution (Å)	2.49
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	POINT
Point Symmetry	C1

Map-Model Fitting and Refinement
Id	1 (7QSN)
Refinement Space	REAL
Refinement Protocol	RIGID BODY FIT
Refinement Target	Cross-correlation coefficient
Overall B Value
Fitting Procedure
Details	Initial rigid-body fitting was done using UCSF ChimeraX fit in map tool, with modifications made in Coot, followed by successive rounds of real-space ...	Initial rigid-body fitting was done using UCSF ChimeraX fit in map tool, with modifications made in Coot, followed by successive rounds of real-space refinement in PHENIX.

Data Acquisition
Detector Type	GATAN K3 BIOQUANTUM (6k x 4k)
Electron Dose (electrons/Å**2)	40.88

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	TFS KRIOS
Minimum Defocus (nm)	900
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	81000
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details

EM Software
Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21_5207:

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION	Global and local CTF parameters were refined both in cycles in RELION then during refinement cycles in the final homogeneous refinement in cryoSPARC.	1446706	Particles were picked using a bovine complex I 3D reference map (EMD-14127).