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Cryo-EM structure of Streptococcus pneumoniae NADPH oxidase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold Q8CZ28
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 9.487 f_angle_d 0.522 f_chiral_restr 0.037 f_bond_d 0.003 f_plane_restr 0.002
Sample Streptococcus pneumoniae NADPH oxidase with FAD and heme cofactors Sample Components Streptococcus pneumoniae NADPH 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 397972 Reported Resolution (Å) 2.29 Resolution Method FSC 0.143 CUT-OFF Other Details Final refinement was local refinement in cryoSPARC 4.0 using a mask that excludes 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 Fitting Procedure Details
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 PARTICLE SELECTION crYOLO PARTICLE SELECTION Topaz IMAGE ACQUISITION EPU CTF CORRECTION RELION MODEL FITTING UCSF ChimeraX MODEL REFINEMENT PHENIX MODEL REFINEMENT Coot INITIAL EULER ASSIGNMENT cryoSPARC FINAL EULER ASSIGNMENT cryoSPARC CLASSIFICATION cryoSPARC RECONSTRUCTION cryoSPARC
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 8765912 These are the combined particles from two different Topaz models and a crYOLO model and contains duplicate particles.