8OPB
Virus-like Particle based on PVY coat protein with RNA-free helical architecture
ELECTRON MICROSCOPY
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 6HXX | |
| Sample |
|---|
| Virus-like particle from PVY coat protein |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | FILAMENT |
| Vitrification Instrument | |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | HELICAL |
| Number of Particles | 27500 |
| Reported Resolution (Å) | 3.58 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | cryoSPARC Helical refinement with initial helical parameters from Ab initio model and helical layer lines |
| Refinement Type | |
| Symmetry Type | HELICAL |
| Axial Symmetry | C1 |
| Axial Rise | 5.876 |
| Angular Rotation | -48.107 |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 (6HXX) | ||||
| Refinement Space | |||||
| Refinement Protocol | |||||
| Refinement Target | |||||
| Overall B Value | |||||
| Fitting Procedure | |||||
| Details | |||||
| 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 | TFS GLACIOS |
| Minimum Defocus (nm) | 800 |
| Maximum Defocus (nm) | 2100 |
| Minimum Tilt Angle (degrees) | |
| Maximum Tilt Angle (degrees) | |
| Nominal CS | |
| Imaging Mode | BRIGHT FIELD |
| Specimen Holder Model | |
| Nominal Magnification | 150000 |
| Calibrated Magnification | |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 200 |
| Imaging Details |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| PARTICLE SELECTION | cryoSPARC | 3.3 |
| CTF CORRECTION | cryoSPARC | 3.3 |
| MODEL FITTING | Coot | |
| MODEL REFINEMENT | PHENIX | |
| INITIAL EULER ASSIGNMENT | cryoSPARC | 4.1 |
| RECONSTRUCTION | cryoSPARC | 4.1 |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING AND AMPLITUDE CORRECTION | patchCTF correction | 109796 | cryosparc filament tracer | |
