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Cryo-EM structure of Spinacia oleracea cytochrome b6f complex with bound plastocyanin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7QRM experimental model PDB 2PCF
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 12.591 f_angle_d 0.693 f_chiral_restr 0.048 f_bond_d 0.014 f_plane_restr 0.005
Sample cytochrome b6f complex incubated with plastocyanin
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE Sample Vitrification Details
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 87892 Reported Resolution (Å) 3.18 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT
Map-Model Fitting and Refinement Id 1 (7QRM, 2PCF) Refinement Space REAL 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 3.3.1 IMAGE ACQUISITION EPU 2.10.0.1941REL CTF CORRECTION cryoSPARC 3.3.1 MODEL FITTING UCSF ChimeraX 1.7 INITIAL EULER ASSIGNMENT cryoSPARC 3.3.1 CLASSIFICATION RELION 3.1.2 RECONSTRUCTION RELION 3.1.2 MODEL REFINEMENT Coot 0.9.8 MODEL REFINEMENT PHENIX 1.20.1-4487
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 177412 template picker