Cryo-EM structure of SARS-CoV-2 receptor binding domain in complex with SR-23 Fab (local refinement of RBD and Fv)
ELECTRON MICROSCOPY
Refinement
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| f_dihedral_angle_d | 4.631 |
| f_angle_d | 0.497 |
| f_chiral_restr | 0.042 |
| f_plane_restr | 0.005 |
| f_bond_d | 0.003 |
| Sample |
|---|
| SARS-CoV-2 receptor binding domain in complex with SR-23 Fab |
| Sample Components |
| SARS-CoV-2 receptor binding domain |
| SR-23 Fab |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | PARTICLE |
| Vitrification Instrument | FEI VITROBOT MARK IV |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SINGLE PARTICLE |
| Number of Particles | 115041 |
| Reported Resolution (Å) | 2.8 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | |
| Refinement Type | |
| Symmetry Type | POINT |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 | ||||
| Refinement Space | REAL | ||||
| Refinement Protocol | RIGID BODY FIT | ||||
| Refinement Target | |||||
| Overall B Value | |||||
| Fitting Procedure | |||||
| Details | |||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | GATAN K3 BIOCONTINUUM (6k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 67.6 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | TFS KRIOS |
| Minimum Defocus (nm) | 700 |
| Maximum Defocus (nm) | 1700 |
| Minimum Tilt Angle (degrees) | |
| Maximum Tilt Angle (degrees) | |
| Nominal CS | |
| Imaging Mode | BRIGHT FIELD |
| Specimen Holder Model | FEI TITAN KRIOS AUTOGRID HOLDER |
| Nominal Magnification | |
| Calibrated Magnification | 105000 |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 300 |
| Imaging Details |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| PARTICLE SELECTION | cryoSPARC | 4.2.1 |
| PARTICLE SELECTION | Topaz | 0.2.5 |
| MODEL FITTING | UCSF ChimeraX | tech preview |
| CLASSIFICATION | cryoSPARC | 4.2.1 |
| RECONSTRUCTION | cryoSPARC | 4.2.1 |
| MODEL REFINEMENT | PHENIX | 1.20.1-4487 |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING AND AMPLITUDE CORRECTION | 2200000 | |||
