ELECTRON MICROSCOPY
| Sample |
|---|
| yeast NPC |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | CELL |
| Vitrification Instrument | |
| Cryogen Name | ETHANE-PROPANE |
| Sample Vitrification Details | A custom-built vitrification device (Max Planck Institute for Biochemistry, Munich) |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SUBTOMOGRAM AVERAGING |
| Number of Particles | 518 |
| Reported Resolution (Å) | 37 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | |
| Refinement Type | |
| Symmetry Type | POINT |
| Point Symmetry | C8 |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 | ||||
| Refinement Space | REAL | ||||
| Refinement Protocol | FLEXIBLE FIT | ||||
| Refinement Target | cross-correlation | ||||
| Overall B Value | |||||
| Fitting Procedure | |||||
| Details | Manual docking and limited molecular dynamics flexible fitting | ||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | GATAN K2 SUMMIT (4k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 4.5 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | FEI TITAN KRIOS |
| Minimum Defocus (nm) | 2500 |
| Maximum Defocus (nm) | 6000 |
| Minimum Tilt Angle (degrees) | |
| Maximum Tilt Angle (degrees) | |
| Nominal CS | |
| Imaging Mode | BRIGHT FIELD |
| Specimen Holder Model | |
| Nominal Magnification | 42000 |
| Calibrated Magnification | |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 300 |
| Imaging Details | Tilt series collection: dose-symmetric & bi-directional |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| IMAGE ACQUISITION | SerialEM | |
| CTF CORRECTION | EMAN2 | 2.9 |
| MODEL FITTING | UCSF Chimera | 1.14 |
| MODEL REFINEMENT | VMD | 1.9.3 |
| RECONSTRUCTION | EMAN2 | 2.9 |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING ONLY | e2spt_ctf.py was used to identify the precise z height of the particle in the tomogram. This precise height was then used for computing the CTF and performing the CTF correction. | |||
