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Cryo-EM structure of Na+-translocating NADH-ubiquinone oxidoreductase NqrB-G141A mutant from Vibrio cholerae reduced by NADH, with bound korormicin A, shifted state
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9LRR
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 12.658 f_angle_d 0.584 f_chiral_restr 0.043 f_plane_restr 0.005 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 74083 Reported Resolution (Å) 2.93 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 (9LRR) Refinement Space REAL Refinement Protocol OTHER Refinement Target Overall B Value Fitting Procedure Details The hydrophilic moiety of NqrC is fitted by rigid body fitting.
The other is fitted by flexible 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 0.001864 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 cryoSPARC 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_5207
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details NONE 1384337