7QDG
SARS-CoV-2 S protein S:A222V + S:D614G mutant 1-up
ELECTRON MICROSCOPY
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 7BNN | |
Refinement
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 29.394 |
| r_long_range_B_refined | 18.718 |
| r_long_range_B_other | 18.718 |
| r_dihedral_angle_3_deg | 15.483 |
| r_dihedral_angle_4_deg | 13.711 |
| r_mcangle_it | 7.001 |
| r_mcangle_other | 7.001 |
| r_scangle_other | 5.597 |
| r_dihedral_angle_1_deg | 3.821 |
| r_mcbond_it | 3.809 |
| Sample |
|---|
| SARS-CoV-2 S protein S:A222V + S:D614G mutant |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | PARTICLE |
| Vitrification Instrument | LEICA EM GP |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SINGLE PARTICLE |
| Number of Particles | 145681 |
| Reported Resolution (Å) | 3.4 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | |
| Refinement Type | |
| Symmetry Type | POINT |
| Point Symmetry | C1 |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 (7BNN) | ||||
| Refinement Space | RECIPROCAL | ||||
| Refinement Protocol | OTHER | ||||
| Refinement Target | |||||
| Overall B Value | |||||
| Fitting Procedure | |||||
| Details | |||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | FEI FALCON III (4k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 32.4 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | FEI TALOS ARCTICA |
| Minimum Defocus (nm) | 300 |
| Maximum Defocus (nm) | 3500 |
| Minimum Tilt Angle (degrees) | |
| Maximum Tilt Angle (degrees) | |
| Nominal CS | |
| Imaging Mode | OTHER |
| Specimen Holder Model | FEI TITAN KRIOS AUTOGRID HOLDER |
| Nominal Magnification | 120000 |
| Calibrated Magnification | |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 200 |
| Imaging Details |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| PARTICLE SELECTION | crYOLO | |
| PARTICLE SELECTION | Scipion | |
| IMAGE ACQUISITION | EPU | |
| CTF CORRECTION | CTFFIND | |
| CTF CORRECTION | Gctf | |
| CTF CORRECTION | cryoSPARC | |
| MODEL FITTING | UCSF Chimera | |
| MODEL FITTING | Coot | |
| MODEL REFINEMENT | REFMAC | |
| INITIAL EULER ASSIGNMENT | cryoSPARC | |
| FINAL EULER ASSIGNMENT | cryoSPARC | |
| CLASSIFICATION | RELION | |
| CLASSIFICATION | Scipion | |
| RECONSTRUCTION | cryoSPARC | |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING AND AMPLITUDE CORRECTION | 509466 | |||
