8QQM
nicotinic acetylcholine receptor in intact synaptic membrane
ELECTRON MICROSCOPY
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 7SMM | |
| Sample |
|---|
| Muscle-type nicotinic acetylcholine receptor in intact synaptic membrane |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | HELICAL ARRAY |
| Vitrification Instrument | HOMEMADE PLUNGER |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SINGLE PARTICLE |
| Number of Particles | 107524 |
| Reported Resolution (Å) | 4.7 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | The volumes for FSC determination were cut out from helical reconstructions of each class average |
| Refinement Type | |
| Symmetry Type | POINT |
| Point Symmetry | C1 |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 (7SMM, 7SMM, 7SMM, 7SMM, 7SMM) | ||||
| Refinement Space | REAL | ||||
| Refinement Protocol | FLEXIBLE FIT | ||||
| Refinement Target | |||||
| Overall B Value | 350 | ||||
| Fitting Procedure | |||||
| Details | Refinement parameters were chosen to minimise changes to the original secondary structure | ||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | FEI FALCON III (4k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 40 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | FEI TITAN KRIOS |
| Minimum Defocus (nm) | 1200 |
| Maximum Defocus (nm) | 2800 |
| 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 | 59000 |
| Calibrated Magnification | 104478 |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 300 |
| Imaging Details | All images taken manually: by searching at low magnification for long straight and narrow tubes, then recording in integrating mode |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| PARTICLE SELECTION | RELION | 2.1 and 3.1 |
| IMAGE ACQUISITION | DigitalMicrograph | |
| CTF CORRECTION | Gctf | |
| MODEL FITTING | DireX | |
| CLASSIFICATION | RELION | 2.1 |
| RECONSTRUCTION | RELION | 2.1 |
| MODEL REFINEMENT | DireX | |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING AND AMPLITUDE CORRECTION | Correction performed by standard procedure in RELION | 160652 | 160652 tube segments from 4045 selected micrographs were reduced to 107524 tube segments after 2D classification | |
