5I08
Prefusion structure of a human coronavirus spike protein
ELECTRON MICROSCOPY
| Sample |
|---|
| HKU1 spike with attached foldon domain and mutated furin-cleavage site |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | PARTICLE |
| Vitrification Instrument | HOMEMADE PLUNGER |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | 3 uL sample was applied to grid, blotted, and plunged into liquid ethane. |
| Staining Type | NEGATIVE |
| Staining Material | uranyl formate |
| Staining Details | 3 uL sample was applied to grid for 30 seconds and then blotted. Grids were stained with 3 uL 1% uranyl formate for 60 seconds followed by blotting. |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SINGLE PARTICLE |
| Number of Particles | 31435 |
| Reported Resolution (Å) | 4.04 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | |
| Refinement Type | |
| Symmetry Type | POINT |
| Point Symmetry | C3 |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 | ||||
| Refinement Space | REAL | ||||
| Refinement Protocol | AB INITIO MODEL | ||||
| Refinement Target | EMRinger | ||||
| Overall B Value | 117 | ||||
| Fitting Procedure | |||||
| Details | Model building and refinement were conducted using a combination of software programs. | ||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | GATAN K2 SUMMIT (4k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 57 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | FEI TITAN KRIOS |
| Minimum Defocus (nm) | 1000 |
| Maximum Defocus (nm) | 3500 |
| Minimum Tilt Angle (degrees) | |
| Maximum Tilt Angle (degrees) | |
| Nominal CS | |
| Imaging Mode | BRIGHT FIELD |
| Specimen Holder Model | FEI TITAN KRIOS AUTOGRID HOLDER |
| Nominal Magnification | 22500 |
| Calibrated Magnification | 22500 |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 300 |
| Imaging Details |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| PARTICLE SELECTION | DoG Picker | |
| PARTICLE SELECTION | FindEM | |
| IMAGE ACQUISITION | Leginon | |
| CTF CORRECTION | CTFFIND3 | |
| MODEL FITTING | MODELLER | |
| MODEL FITTING | Rosetta | 2015.19 |
| MODEL FITTING | Coot | 0.8.2 |
| INITIAL EULER ASSIGNMENT | RELION | 1.3 |
| FINAL EULER ASSIGNMENT | RELION | 1.4b1 |
| CLASSIFICATION | IMAGIC | |
| RECONSTRUCTION | RELION | 1.4b1 |
| MODEL REFINEMENT | Rosetta | 2015.19 |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING AND AMPLITUDE CORRECTION | 39164 | 2188 particles were selected from a subset of the data using DoG Picker. These particles were used to generate a 3D model from which back projections were derived. Back projection images were used as templates for picking particles from the entire dataset using FindEM. | ||
