8U18
Cryo-EM structure of murine Thrombopoietin receptor ectodomain in complex with Tpo
ELECTRON MICROSCOPY
Refinement
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| f_dihedral_angle_d | 9.94 |
| f_angle_d | 0.728 |
| f_chiral_restr | 0.044 |
| f_plane_restr | 0.006 |
| f_bond_d | 0.004 |
| Sample |
|---|
| 2:1 complex of the mouse thrombopoietin receptor ectodomain and mouse thrombopoietin |
| Sample Components |
| mouse thrombopoietin receptor ectodomain |
| mouse thrombopoietin |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | PARTICLE |
| Vitrification Instrument | FEI VITROBOT MARK IV |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | Blot time of 4 s, blot force of 6 and no wait time or drain time. |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SINGLE PARTICLE |
| Number of Particles | 745000 |
| Reported Resolution (Å) | 3.6 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | Final map was generated using Non-uniform refinement followed by 3DFlex refinement in cryoSPARC. Map was sharpened by deepEMhancer. |
| Refinement Type | |
| Symmetry Type | POINT |
| Point Symmetry | C1 |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 | ||||
| Refinement Space | REAL | ||||
| Refinement Protocol | FLEXIBLE FIT | ||||
| Refinement Target | Cross-correlation coefficient | ||||
| Overall B Value | |||||
| Fitting Procedure | |||||
| Details | ChimeraX was used to perform rigid-body fitting of domains and modelling was performed using Coot and ISOLDE. Refinement was carried out in PHENIX. | ||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | GATAN K3 BIOQUANTUM (6k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 50.57 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | FEI TITAN KRIOS |
| Minimum Defocus (nm) | 400 |
| Maximum Defocus (nm) | 3600 |
| 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 | 130000 |
| Calibrated Magnification | |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 300 |
| Imaging Details |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| PARTICLE SELECTION | cryoSPARC | 4.2.1 |
| IMAGE ACQUISITION | EPU | 2 |
| CTF CORRECTION | cryoSPARC | 4.2.1 |
| MODEL FITTING | ISOLDE | 1.6.0 |
| MODEL FITTING | UCSF ChimeraX | 1.6.1 |
| MODEL FITTING | Coot | 0.9.8.3 |
| INITIAL EULER ASSIGNMENT | cryoSPARC | 4.2.1 |
| FINAL EULER ASSIGNMENT | cryoSPARC | 4.2.1 |
| 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 | |
| NONE | Defocus values were estimated using patch CTF estimation and CTF correction was performed during 3D reccnstruction. | 2353523 | Templates for picking were generated using a gaussian based picking approach, followed by 2D classification and selection of high-quality 2D classes for template picking. | |
