7Z7X
CRYO-EM STRUCTURE OF SARS-COV-2 SPIKE : H11-H6 nanobody complex
ELECTRON MICROSCOPY
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 6ZHD | |
Refinement
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| f_dihedral_angle_d | 6.5069 |
| f_angle_d | 0.6022 |
| f_chiral_restr | 0.047 |
| f_bond_d | 0.006 |
| f_plane_restr | 0.004 |
| Sample |
|---|
| Complex between Spike and nanobody H11-H6 |
| Sample Components |
| Spike glycoprotein trimer with fibritin tag |
| Nanobody H11-H6 |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | PARTICLE |
| Vitrification Instrument | SPOTITON |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | SPT Labtech prototype 300 mesh 1.2/2.0 nanowire grids with a highly reproduceable rectangular bar cross-section were used. The grids were glow-dischar ... |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SINGLE PARTICLE |
| Number of Particles | 210571 |
| Reported Resolution (Å) | 3.3 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | |
| Refinement Type | |
| Symmetry Type | POINT |
| Point Symmetry | C1 |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 (6ZHD, 6ZHD, 6ZHD) | ||||
| Refinement Space | RECIPROCAL | ||||
| 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 | TFS 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 | FEI TITAN KRIOS AUTOGRID HOLDER |
| Nominal Magnification | 81000 |
| Calibrated Magnification | |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 300 |
| Imaging Details | EPU auto-function coma free correction |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| PARTICLE SELECTION | RELION | 3.08 |
| IMAGE ACQUISITION | EPU | |
| CTF CORRECTION | Gctf | |
| MODEL FITTING | UCSF Chimera | |
| MODEL FITTING | Coot | |
| INITIAL EULER ASSIGNMENT | RELION | 3.08 |
| FINAL EULER ASSIGNMENT | RELION | 3.08 |
| CLASSIFICATION | RELION | 3.08 |
| RECONSTRUCTION | RELION | 3.08 |
| MODEL REFINEMENT | PHENIX | |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING AND AMPLITUDE CORRECTION | 1609112 | |||
