8QT9
Cryo-EM structure of stably reduced Streptococcus pneumoniae NADPH oxidase in complex with NADH
ELECTRON MICROSCOPY
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. | ||
