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Cryo-EM structure of stably reduced Streptococcus pneumoniae NADPH oxidase in complex with NADH
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 10.815 f_angle_d 0.627 f_chiral_restr 0.048 f_bond_d 0.003 f_plane_restr 0.003
Sample Streptococcus pneumoniae NADPH oxidase with FAD and heme cofactors and NADH bound
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 697211 Reported Resolution (Å) 2.36 Resolution Method FSC 0.143 CUT-OFF Other Details Final refinement is local refinement in cryoSPARC 4.0 using a tight mask excluding the detergent micelle. Refinement Type Symmetry Type POINT
Map-Model Fitting and Refinement Id 1 Refinement Space REAL Refinement Protocol RIGID BODY FIT Refinement Target Cross-correlation coefficient Overall B Value 26.54 Fitting Procedure Details Model was fit using ChimeraX. Coot and PHENIX were used for model refinement.
Data Acquisition Detector Type FEI FALCON IV (4k x 4k) Electron Dose (electrons/Å**2) 70
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model TFS KRIOS Minimum Defocus (nm) 700 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 215000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version MODEL FITTING UCSF ChimeraX MODEL REFINEMENT Coot MODEL REFINEMENT PHENIX
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 14339155 These are the combined particles from two different Topaz models and a crYOLO model and contains duplicate particles.