ELECTRON MICROSCOPY
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 6XKL | |
Refinement
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| f_dihedral_angle_d | 3.055 |
| f_angle_d | 0.381 |
| f_chiral_restr | 0.038 |
| f_plane_restr | 0.003 |
| f_bond_d | 0.001 |
| Sample |
|---|
| Structure of a SARS-CoV-2 spike S2 subunit in a pre-fusion, open conformation in complex with the 6C10 Fab |
| Sample Components |
| Fab fragment of the 6C10 human monoclonal antibody |
| Structure of a SARS-CoV-2 spike S2 subunit in a pre-fusion, open conformation |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | PARTICLE |
| Vitrification Instrument | FEI VITROBOT MARK IV |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | 6 seconds blotting time at force 0 |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SINGLE PARTICLE |
| Number of Particles | 408064 |
| Reported Resolution (Å) | 2.93 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | |
| Refinement Type | |
| Symmetry Type | POINT |
| Point Symmetry | C3 |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 (6xkl) | 2 (6xkl) | |||
| Refinement Space | REAL | ||||
| Refinement Protocol | OTHER | OTHER | |||
| Refinement Target | Cross-correlation coefficient | ||||
| Overall B Value | 150 | ||||
| Fitting Procedure | |||||
| Details | COOT model building and refinament | ||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | GATAN K3 BIOQUANTUM (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) | 600 |
| Maximum Defocus (nm) | 1800 |
| 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 | 75000 |
| Calibrated Magnification | 75757 |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 300 |
| Imaging Details |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| PARTICLE SELECTION | Warp | 1.09 |
| IMAGE ACQUISITION | EPU | 2.12 |
| CTF CORRECTION | Warp | 1.09 |
| INITIAL EULER ASSIGNMENT | cryoSPARC | 4.0 |
| FINAL EULER ASSIGNMENT | cryoSPARC | 4.0 |
| CLASSIFICATION | cryoSPARC | 4.0 |
| RECONSTRUCTION | cryoSPARC | 4.0 |
| MODEL REFINEMENT | PHENIX | 1.20.1_4487:1.21 |
| MODEL REFINEMENT | Coot | 0.9.5 |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING AND AMPLITUDE CORRECTION | 407314 | |||
