8BGW
CryoEM structure of quinol-dependent Nitric Oxide Reductase (qNOR) from Alcaligenes xylosoxidans at 2.2 A resolution
ELECTRON MICROSCOPY
Refinement
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 33.71 |
| r_dihedral_angle_3_deg | 16.396 |
| r_dihedral_angle_4_deg | 16.157 |
| r_lrange_it | 13.388 |
| r_lrange_other | 13.388 |
| r_scangle_it | 9.63 |
| r_scangle_other | 9.629 |
| r_mcangle_it | 8.426 |
| r_mcangle_other | 8.425 |
| r_dihedral_angle_1_deg | 6.941 |
| Sample |
|---|
| quinol-dependent Nitric Oxide Reductase |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | PARTICLE |
| Vitrification Instrument | FEI VITROBOT MARK IV |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | Sample at 3 mg/mL was applied to glow-discharged Quantifoil Au R1.2/1.3 holey carbo grids |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SINGLE PARTICLE |
| Number of Particles | 404950 |
| Reported Resolution (Å) | 2.2 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | |
| Refinement Type | |
| Symmetry Type | POINT |
| Point Symmetry | C2 |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 | ||||
| Refinement Space | RECIPROCAL | ||||
| Refinement Protocol | RIGID BODY FIT | ||||
| Refinement Target | Cross-correlation coefficient | ||||
| Overall B Value | 47 | ||||
| Fitting Procedure | |||||
| Details | |||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | FEI FALCON IV (4k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 34.9 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | FEI TITAN KRIOS |
| Minimum Defocus (nm) | 900 |
| Maximum Defocus (nm) | 2700 |
| 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 | 130000 |
| Calibrated Magnification | |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 300 |
| Imaging Details |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| PARTICLE SELECTION | crYOLO | 1.6.1 |
| IMAGE ACQUISITION | EPU | 2.14 |
| CTF CORRECTION | CTFFIND | 4.1 |
| MODEL FITTING | MOLREP | 11.06.04 |
| MODEL REFINEMENT | REFMAC | 5.8.0267 |
| MODEL REFINEMENT | PHENIX | 1.2 |
| INITIAL EULER ASSIGNMENT | RELION | 3.1 |
| FINAL EULER ASSIGNMENT | RELION | 3.1 |
| CLASSIFICATION | RELION | 3.1 |
| RECONSTRUCTION | RELION | 3.1 |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING AND AMPLITUDE CORRECTION | 3000000 | |||
