8OPD
Virus-like Particle based on PVY coat protein with dC40 deletion with stacked-ring architecture
ELECTRON MICROSCOPY
| Sample |
|---|
| Virus-like particle from dC40 coat protein |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | FILAMENT |
| Vitrification Instrument | |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | HELICAL |
| Number of Particles | 399617 |
| Reported Resolution (Å) | 3.5 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | Final cryoEM map was obtained by Phenix density modification. |
| Refinement Type | |
| Symmetry Type | HELICAL |
| Axial Symmetry | C8 |
| Axial Rise | 43.29 |
| Angular Rotation | 15.04 |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 | ||||
| Refinement Space | |||||
| Refinement Protocol | |||||
| Refinement Target | |||||
| Overall B Value | |||||
| Fitting Procedure | |||||
| Details | |||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | FEI FALCON II (4k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 84 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | TFS KRIOS |
| Minimum Defocus (nm) | 400 |
| Maximum Defocus (nm) | 1300 |
| Minimum Tilt Angle (degrees) | |
| Maximum Tilt Angle (degrees) | |
| Nominal CS | |
| Imaging Mode | BRIGHT FIELD |
| Specimen Holder Model | |
| Nominal Magnification | 75000 |
| Calibrated Magnification | |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 300 |
| Imaging Details |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| PARTICLE SELECTION | crYOLO | |
| IMAGE ACQUISITION | EPU | |
| CTF CORRECTION | CTFFIND | 4.1 |
| MODEL FITTING | Coot | |
| MODEL REFINEMENT | PHENIX | 1.20 |
| CLASSIFICATION | RELION | |
| RECONSTRUCTION | RELION | |
| RECONSTRUCTION | PHENIX | |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING AND AMPLITUDE CORRECTION | 2966850 | CrYOLO filament picking based on pre-trained neural network model | ||
