7W5Z | pdb_00007w5z

Cryo-EM structure of Tetrahymena thermophila mitochondrial complex IV, composite dimer model

ELECTRON MICROSCOPY

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Refinement

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	10.8504
f_angle_d	0.4866
f_chiral_restr	0.0405
f_plane_restr	0.0039
f_bond_d	0.0033

Sample
Cytochrome c oxidase dimer

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	FEI VITROBOT MARK III
Cryogen Name	ETHANE
Sample Vitrification Details	incubation time before blotting: 60s blot time: 9s blot force: 25 offset: -2 incubation after blotting: 0s

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	394262
Reported Resolution (Å)	3.02
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	RIGID BODY FIT
Refinement Target
Overall B Value
Fitting Procedure
Details

Data Acquisition
Detector Type	GATAN K3 (6k x 4k)
Electron Dose (electrons/Å**2)	60

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	TFS GLACIOS
Minimum Defocus (nm)	500
Maximum Defocus (nm)	3000
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
Calibrated Magnification	56818
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	200
Imaging Details

EM Software
Task	Software Package	Version
PARTICLE SELECTION	crYOLO	1.7.6
IMAGE ACQUISITION	SerialEM
CTF CORRECTION	CTFFIND	4.1
MODEL FITTING	UCSF Chimera
MODEL FITTING	Coot
INITIAL EULER ASSIGNMENT	cryoSPARC	3.2.0
FINAL EULER ASSIGNMENT	cryoSPARC	3.2.0
CLASSIFICATION	cryoSPARC	3.2.0
RECONSTRUCTION	cryoSPARC	3.2.0
MODEL REFINEMENT	PHENIX	1.19.2

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION		1798857