8PE4
Capsid structure of the L-A helper virus from native viral communities
ELECTRON MICROSCOPY
| Sample |
|---|
| Saccharomyces cerevisiae virus L-A |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | PARTICLE |
| Vitrification Instrument | FEI VITROBOT MARK IV |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | blot force 2 and blot time 6 s before plunging |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SINGLE PARTICLE |
| Number of Particles | 12974 |
| Reported Resolution (Å) | 3.21 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | |
| Refinement Type | |
| Symmetry Type | POINT |
| Point Symmetry | I |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 (1M1C) | ||||
| Refinement Space | REAL | ||||
| Refinement Protocol | RIGID BODY FIT | ||||
| Refinement Target | |||||
| Overall B Value | |||||
| Fitting Procedure | |||||
| Details | The initial model was rigid-fitted by ChimeraX and refined by iterative cycles of Coot and PHENIX. | ||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | FEI FALCON IV (4k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 30 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | TFS GLACIOS |
| Minimum Defocus (nm) | 1000 |
| Maximum Defocus (nm) | 2000 |
| 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 | 92000 |
| Calibrated Magnification | 89297 |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 200 |
| Imaging Details |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| PARTICLE SELECTION | cryoSPARC | v3.3 |
| IMAGE ACQUISITION | EPU | 2.8 |
| CTF CORRECTION | cryoSPARC | v.3.3 |
| MODEL FITTING | UCSF ChimeraX | 1.3 |
| CLASSIFICATION | cryoSPARC | v3.3 |
| RECONSTRUCTION | cryoSPARC | v3.3 |
| MODEL REFINEMENT | Coot | 0.9.6 |
| MODEL REFINEMENT | PHENIX | 1.21rc1 |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| NONE | 7840838 | Particles were selected using cryoSPARC blob picker with 500 A diameter and 0.5x diameter inter-particle distance. | ||
