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Cryo-EM structure of the reduced cytochrome bd oxidase from M. tuberculosis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7NKZ
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 13.495 f_angle_d 0.858 f_chiral_restr 0.071 f_plane_restr 0.004 f_bond_d 0.003
Sample Cytochrome BD-I oxidase
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK III Cryogen Name ETHANE Sample Vitrification Details
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 1277019 Reported Resolution (Å) 2.96 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 (7NKZ) Refinement Space REAL Refinement Protocol BACKBONE TRACE Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type GATAN K3 BIOQUANTUM (6k x 4k) Electron Dose (electrons/Å**2) 100
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model TFS KRIOS Minimum Defocus (nm) 1000 Maximum Defocus (nm) 2400 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 4.3.0 IMAGE ACQUISITION EPU 2.1.0 CTF CORRECTION cryoSPARC 4.3.0 MODEL FITTING UCSF ChimeraX 1.7.1 MODEL REFINEMENT UCSF ChimeraX 1.7.1 MODEL REFINEMENT Coot 0.89 MODEL REFINEMENT PHENIX 1.21.1 FINAL EULER ASSIGNMENT cryoSPARC 4.3.0 CLASSIFICATION cryoSPARC 4.3.0 RECONSTRUCTION cryoSPARC 4.3.0
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 15300000