Experiment: 7ZYV

Cryo-EM structure of catalytically active Spinacia oleracea cytochrome b6f in complex with endogenous plastoquinones at 2.13 A resolution

ELECTRON MICROSCOPY

Starting Model(s)

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

Sample
Cytochrome b6f complex

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	FEI VITROBOT MARK IV
Cryogen Name	ETHANE
Sample Vitrification Details	blot time 2 s, wait time 0 s, blot force -1

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	685979
Reported Resolution (Å)	2.13
Resolution Method	FSC 0.143 CUT-OFF
Other Details	Non-uniform Refinement
Refinement Type
Symmetry Type	POINT
Point Symmetry	C2

Map-Model Fitting and Refinement
Id	1 (7QRM)
Refinement Space
Refinement Protocol	RIGID BODY FIT
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	TFS KRIOS
Minimum Defocus (nm)	900
Maximum Defocus (nm)	2100
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	105000
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details

EM Software
Task	Software Package	Version
PARTICLE SELECTION	cryoSPARC	v3.3.1
IMAGE ACQUISITION	EPU	2.10
CTF CORRECTION	cryoSPARC	v3.3.1
MODEL FITTING	UCSF ChimeraX
MODEL REFINEMENT	PHENIX
INITIAL EULER ASSIGNMENT	cryoSPARC	v3.3.1
FINAL EULER ASSIGNMENT	cryoSPARC	v3.3.1
CLASSIFICATION	cryoSPARC	v3.3.1
RECONSTRUCTION	cryoSPARC	v3.3.1

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION	Non-uniform Refinement with iterative global CTF refinement and anisotropic magnification fitting	42951	given number of particles is after blob picker and 2D cleaning