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cytochrome bd-II type oxidase with bound aurachin D
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6RX4
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 11.536 f_angle_d 0.684 f_chiral_restr 0.039 f_bond_d 0.003 f_plane_restr 0.003
Sample Cytochrome bd-II ubiquinol oxidase
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE Sample Vitrification Details 45 sec incubation, 6.5 sec blotting
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 125497 Reported Resolution (Å) 3 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C2
Map-Model Fitting and Refinement Id 1 (6RX4) Refinement Space REAL Refinement Protocol FLEXIBLE FIT Refinement Target WEIGHTED MAP SUM AT ATOM CENTERS Overall B Value 94 Fitting Procedure Details
Data Acquisition Detector Type FEI FALCON III (4k x 4k) Electron Dose (electrons/Å**2) 79
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) 1400 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 75000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION RELION 3.1 IMAGE ACQUISITION EPU CTF CORRECTION CTFFIND 4.1 MODEL FITTING Coot 0.8.9 INITIAL EULER ASSIGNMENT RELION 3.1 FINAL EULER ASSIGNMENT RELION 3.1 CLASSIFICATION RELION 3.1 RECONSTRUCTION RELION 3.1 MODEL REFINEMENT PHENIX 19-4092
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 800000