ELECTRON MICROSCOPY
Refinement
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| f_dihedral_angle_d | 4.065 |
| f_angle_d | 0.41 |
| f_chiral_restr | 0.036 |
| f_plane_restr | 0.003 |
| f_bond_d | 0.002 |
| Sample |
|---|
| PKD2 ion channel F629S variant protomer |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | PARTICLE |
| Vitrification Instrument | LEICA EM GP |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | Vitrification carried in air. Ethane temperature -183 C |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SINGLE PARTICLE |
| Number of Particles | 215875 |
| Reported Resolution (Å) | 2.76 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | Final reconstruction performed with C4 symmetry imposed |
| Refinement Type | |
| Symmetry Type | POINT |
| Point Symmetry | C4 |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 | ||||
| Refinement Space | REAL | ||||
| Refinement Protocol | |||||
| Refinement Target | |||||
| Overall B Value | 107.9 | ||||
| Fitting Procedure | |||||
| Details | The initial Alphafold model was fitted to the map using ChimeraX. Refinement was performed using ISOLDE and PHENIX. | ||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | GATAN K3 (6k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 60 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | TFS KRIOS |
| Minimum Defocus (nm) | 600 |
| Maximum Defocus (nm) | 2400 |
| 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 | 4.5 |
| IMAGE ACQUISITION | SerialEM | v4.1.0beta |
| CTF CORRECTION | cryoSPARC | 4.5 |
| MODEL FITTING | UCSF ChimeraX | 1.8 |
| MODEL FITTING | ISOLDE | 1.8 |
| INITIAL EULER ASSIGNMENT | cryoSPARC | 4.5 |
| FINAL EULER ASSIGNMENT | cryoSPARC | 4.5 |
| CLASSIFICATION | cryoSPARC | |
| RECONSTRUCTION | cryoSPARC | 4.5 |
| MODEL REFINEMENT | ISOLDE | 1.8 |
| MODEL REFINEMENT | PHENIX | 1.21.2 |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING AND AMPLITUDE CORRECTION | 1046126 | Denoised micrographs were blob picked (130-170 angstrom) | ||
