7Y6D
Cryo-EM structure of SARS-CoV-2 Delta variant spike proteins on intact virions: 3 Closed RBD
ELECTRON MICROSCOPY
| Sample |
|---|
| Severe acute respiratory syndrome coronavirus 2 |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | PARTICLE |
| Vitrification Instrument | GATAN CRYOPLUNGE 3 |
| Cryogen Name | NITROGEN |
| Sample Vitrification Details | |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SINGLE PARTICLE |
| Number of Particles | 45252 |
| Reported Resolution (Å) | 4.39 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | |
| Refinement Type | |
| Symmetry Type | POINT |
| Point Symmetry | C3 |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 (7SBK, 6XR8) | ||||
| Refinement Space | REAL | ||||
| Refinement Protocol | |||||
| Refinement Target | |||||
| Overall B Value | 118.79 | ||||
| Fitting Procedure | |||||
| Details | |||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | GATAN K3 (6k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 50 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | FEI TITAN KRIOS |
| Minimum Defocus (nm) | 1000 |
| Maximum Defocus (nm) | 3000 |
| Minimum Tilt Angle (degrees) | |
| Maximum Tilt Angle (degrees) | |
| Nominal CS | 2.7 |
| Imaging Mode | BRIGHT FIELD |
| Specimen Holder Model | |
| Nominal Magnification | 81000 |
| Calibrated Magnification | |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 300 |
| Imaging Details |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| PARTICLE SELECTION | RELION | 3.1.0 |
| CTF CORRECTION | RELION | 3.1.0 |
| MODEL FITTING | Coot | 0.9.6 |
| MODEL REFINEMENT | PHENIX | 1.20.1 |
| INITIAL EULER ASSIGNMENT | RELION | 3.1.0 |
| FINAL EULER ASSIGNMENT | RELION | 3.1.0 |
| RECONSTRUCTION | RELION | 3.1.0 |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING AND AMPLITUDE CORRECTION | CTFs are applied to the projections of the map during 3D classification and 3D refinement. | 674792 | Initial micrographs were deconvolved using Warp, and 7,950 spikes were manually picked from 474 micrographs for training Topaz neural network. The trained Topaz neural network was used to automatically pick the spikes. 674,792 particles were auto-picked by Topaz. | |
