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Cryo-EM structure of Na+-translocating NADH-ubiquinone oxidoreductase from Vibrio cholerae reduced by NADH, in the absence of Na+, middle state
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7XK3
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 8.871 f_angle_d 0.607 f_chiral_restr 0.043 f_plane_restr 0.004 f_bond_d 0.003
Sample Na(+)-translocating NADH-quinone reductase
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 100990 Reported Resolution (Å) 3.75 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 (7XK3) Refinement Space REAL Refinement Protocol FLEXIBLE FIT Refinement Target Overall B Value Fitting Procedure Details The hydrophilic region of NqrF was partially modeled by rigid body fitting
Data Acquisition Detector Type GATAN K3 BIOQUANTUM (6k x 4k) Electron Dose (electrons/Å**2) 65
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model TFS KRIOS Minimum Defocus (nm) 800 Maximum Defocus (nm) 1800 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS 0.035 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 PARTICLE SELECTION cryoSPARC v3.3.1 IMAGE ACQUISITION SerialEM 4 CTF CORRECTION cryoSPARC v3.3.1 MODEL FITTING Coot v3.3.1 INITIAL EULER ASSIGNMENT cryoSPARC v3.3.1 FINAL EULER ASSIGNMENT cryoSPARC v3.3.1 CLASSIFICATION cryoSPARC v3.3.1 RECONSTRUCTION cryoSPARC v3.3.1 MODEL REFINEMENT PHENIX 1.21.1_5286
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details NONE 3653368