7AML
RET/GDNF/GFRa1 extracellular complex Cryo-EM structure
ELECTRON MICROSCOPY
Refinement
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| f_dihedral_angle_d | 23.629 |
| f_angle_d | 0.819 |
| f_chiral_restr | 0.057 |
| f_bond_d | 0.005 |
| f_plane_restr | 0.004 |
| Sample |
|---|
| Ternary complex of RET extracellular domain with GDNF and GFRa1 ligand-coreceptor pair |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | PARTICLE |
| Vitrification Instrument | FEI VITROBOT MARK II |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | 90 s wait time, 5 s blot time |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SINGLE PARTICLE |
| Number of Particles | 382547 |
| Reported Resolution (Å) | 3.5 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | |
| Refinement Type | |
| Symmetry Type | POINT |
| Point Symmetry | C2 |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 (7AB8) | ||||
| Refinement Space | REAL | ||||
| Refinement Protocol | FLEXIBLE FIT | ||||
| Refinement Target | |||||
| Overall B Value | |||||
| Fitting Procedure | |||||
| Details | |||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | GATAN K2 SUMMIT (4k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 48.6 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | FEI TITAN KRIOS |
| Minimum Defocus (nm) | 1400 |
| Maximum Defocus (nm) | 3500 |
| Minimum Tilt Angle (degrees) | |
| Maximum Tilt Angle (degrees) | |
| Nominal CS | |
| Imaging Mode | BRIGHT FIELD |
| Specimen Holder Model | FEI TITAN KRIOS AUTOGRID HOLDER |
| Nominal Magnification | 46296 |
| Calibrated Magnification | |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 300 |
| Imaging Details |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| PARTICLE SELECTION | RELION | |
| PARTICLE SELECTION | Gautomatch | |
| IMAGE ACQUISITION | EPU | |
| CTF CORRECTION | CTFFIND | 4.1 |
| MODEL FITTING | PHENIX | 1.18.2 |
| INITIAL EULER ASSIGNMENT | RELION | |
| FINAL EULER ASSIGNMENT | cryoSPARC | 2 |
| CLASSIFICATION | cryoSPARC | 2 |
| RECONSTRUCTION | cryoSPARC | 2 |
| MODEL REFINEMENT | PHENIX | 1.18.2 |
| MODEL REFINEMENT | Coot | |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING AND AMPLITUDE CORRECTION | 2549540 | 1156517 particles picked from 0 tilt data, 1393023 particles picked from 30-degree tilt data | ||
