8J1Q
CryoEM structure of SARS CoV-2 RBD and Aptamer complex
ELECTRON MICROSCOPY
Refinement
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| f_dihedral_angle_d | 33.298 |
| f_angle_d | 1.296 |
| f_chiral_restr | 0.041 |
| f_bond_d | 0.003 |
| f_plane_restr | 0.002 |
| Sample |
|---|
| RBD_Fab_AM032_AM047 complex |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | PARTICLE |
| Vitrification Instrument | FEI VITROBOT MARK IV |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | 2.5 ul of samples placed on grid before plunge frozen with 5s blot time |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SINGLE PARTICLE |
| Number of Particles | 387000 |
| Reported Resolution (Å) | 3.3 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | Final map generated from 3D flex reconstruction following non-uniform refinement. |
| Refinement Type | |
| Symmetry Type | POINT |
| Point Symmetry | C1 |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 (7KGJ, 6XDG, 6XDG) | ||||
| Refinement Space | REAL | ||||
| Refinement Protocol | RIGID BODY FIT | ||||
| Refinement Target | |||||
| Overall B Value | |||||
| Fitting Procedure | |||||
| Details | |||||
| 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) | 800 |
| Maximum Defocus (nm) | 2000 |
| Minimum Tilt Angle (degrees) | |
| Maximum Tilt Angle (degrees) | |
| Nominal CS | 2.73 |
| Imaging Mode | BRIGHT FIELD |
| Specimen Holder Model | FEI TITAN KRIOS AUTOGRID HOLDER |
| Nominal Magnification | 105000 |
| Calibrated Magnification | 105000 |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 300 |
| Imaging Details |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| PARTICLE SELECTION | cryoSPARC | 3.3.2 |
| IMAGE ACQUISITION | EPU | |
| CTF CORRECTION | cryoSPARC | 3.3.2 |
| MODEL FITTING | UCSF Chimera | 1.16 |
| MODEL REFINEMENT | PHENIX | 1.21rc1_4895: |
| MODEL REFINEMENT | Coot | 0.9.6 EL |
| INITIAL EULER ASSIGNMENT | cryoSPARC | 3.3.2 |
| FINAL EULER ASSIGNMENT | cryoSPARC | 3.3.2 |
| CLASSIFICATION | cryoSPARC | 4.0.0 |
| RECONSTRUCTION | cryoSPARC | 4.1.0 and 4.2.1 |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING AND AMPLITUDE CORRECTION | 5448100 | Particles picked using TOPAZ train | ||
