ELECTRON MICROSCOPY
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 6Z43 | |
Refinement
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_long_range_B_refined | 40.206 |
| r_dihedral_angle_2_deg | 30.575 |
| r_mcangle_it | 17.661 |
| r_dihedral_angle_4_deg | 17.032 |
| r_scbond_it | 14.587 |
| r_dihedral_angle_3_deg | 13.385 |
| r_mcbond_it | 10.223 |
| r_dihedral_angle_1_deg | 5.968 |
| r_angle_refined_deg | 1.264 |
| r_chiral_restr | 0.085 |
| Sample |
|---|
| Complex between Spike and nanobody H11-H4 |
| Sample Components |
| Spike |
| nanobody H11-H4 |
| 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 | 126938 |
| Reported Resolution (Å) | 3.7 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | Relion |
| Refinement Type | |
| Symmetry Type | POINT |
| Point Symmetry | C1 |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 (6Z43) | ||||
| Refinement Space | RECIPROCAL | ||||
| Refinement Protocol | RIGID BODY FIT | ||||
| Refinement Target | Correlation | ||||
| Overall B Value | |||||
| Fitting Procedure | |||||
| Details | REFMAC was used via ccpem GUI | ||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | GATAN K3 BIOQUANTUM (6k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 46 | ||||||||
| 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 | 47170 |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 300 |
| Imaging Details | EPU auto-function coma free correction |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| PARTICLE SELECTION | crYOLO | |
| IMAGE ACQUISITION | EPU | 2.6.1 |
| CTF CORRECTION | Gctf | |
| MODEL FITTING | UCSF Chimera | |
| INITIAL EULER ASSIGNMENT | RELION | 3.08 |
| FINAL EULER ASSIGNMENT | RELION | 3.08 |
| CLASSIFICATION | RELION | |
| RECONSTRUCTION | RELION | 3.08 |
| MODEL REFINEMENT | REFMAC | 5 |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING AND AMPLITUDE CORRECTION | Relion | 786392 | ||
