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Cryo-EM structure of Streptococcus pneumoniae NADPH oxidase in complex with NADPH
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 12.092 f_angle_d 0.475 f_chiral_restr 0.037 f_bond_d 0.002 f_plane_restr 0.002
Sample Streptococcus pneumoniae NADPH oxidase with FAD and heme cofactors
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 591137 Reported Resolution (Å) 2.2 Resolution Method FSC 0.143 CUT-OFF Other Details Final refinement was local refinement in cryoSPARC 4.0 with a 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 Fitting Procedure Details Initial model was fit using ChimeraX and refined with Coot and PHENIX.
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 CTFFIND 4.1 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 14458708 These are the combined particles from two different Topaz models and a crYOLO model and contains duplicate particles.