8EVU
Cryo EM structure of Vibrio cholerae NQR
ELECTRON MICROSCOPY
Refinement
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| f_dihedral_angle_d | 8.5388 |
| f_angle_d | 0.4139 |
| f_chiral_restr | 0.039 |
| f_plane_restr | 0.0034 |
| f_bond_d | 0.0021 |
| Sample |
|---|
| Na(+)-translocating NADH-quinone reductase |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | PARTICLE |
| Vitrification Instrument | FEI VITROBOT MARK IV |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | A 3.5 uL droplet of sample was applied to the grid surface and blotted for 4 s before plunging into liquid ethane. |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SINGLE PARTICLE |
| Number of Particles | 106466 |
| Reported Resolution (Å) | 2.5804 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | |
| Refinement Type | |
| Symmetry Type | POINT |
| Point Symmetry | C1 |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 | ||||
| Refinement Space | REAL | ||||
| Refinement Protocol | FLEXIBLE FIT | ||||
| Refinement Target | Cross-correlation | ||||
| Overall B Value | |||||
| Fitting Procedure | |||||
| Details | The model was refined by iterating between manual edits in Coot, molecular dynamics-guided edits using the ISOLDE ChimeraX package, and automated real ... | ||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | GATAN K3 BIOQUANTUM (6k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 50 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | FEI TITAN KRIOS |
| Minimum Defocus (nm) | 800 |
| Maximum Defocus (nm) | 3200 |
| 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 | 81000 |
| Calibrated Magnification | |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 300 |
| Imaging Details |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| PARTICLE SELECTION | Topaz | 0.2.5 |
| IMAGE ACQUISITION | EPU | 2.9 |
| CTF CORRECTION | CTFFIND | 4.1.14 |
| CTF CORRECTION | RELION | 4.0beta2 |
| MODEL FITTING | UCSF Chimera | |
| INITIAL EULER ASSIGNMENT | RELION | 4.0beta2 |
| CLASSIFICATION | RELION | 4.0beta2 |
| RECONSTRUCTION | RELION | 4.0beta2 |
| MODEL REFINEMENT | PHENIX | |
| MODEL REFINEMENT | ISOLDE | |
| MODEL REFINEMENT | Rosetta | |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING AND AMPLITUDE CORRECTION | 304335 | |||
