Structure of human NHE6.1 bound to PIP2 (core-TM domain)
ELECTRON MICROSCOPY
Refinement
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| f_dihedral_angle_d | 13.1344 |
| f_angle_d | 0.6393 |
| f_chiral_restr | 0.0397 |
| f_plane_restr | 0.0054 |
| f_bond_d | 0.0037 |
| Sample |
|---|
| NHE6.1 homodimer |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | PARTICLE |
| Vitrification Instrument | FEI VITROBOT MARK IV |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | Sample vol 3ul; blot force -5; Blot time 9s; Wait time 20sec |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SINGLE PARTICLE |
| Number of Particles | 153800 |
| Reported Resolution (Å) | 2.33 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | cryoSPARC non-uniform refinement of CROSIEVED particles |
| Refinement Type | |
| Symmetry Type | POINT |
| Point Symmetry | C1 |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 | ||||
| Refinement Space | REAL | ||||
| Refinement Protocol | FLEXIBLE FIT | ||||
| Refinement Target | |||||
| Overall B Value | |||||
| Fitting Procedure | |||||
| Details | Initial model fitted and manually rebuilt/refined in COOT and final refinement in ISOLDE and PHENIX | ||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | TFS FALCON 4i (4k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 50 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | TFS KRIOS |
| Minimum Defocus (nm) | 800 |
| Maximum Defocus (nm) | 2200 |
| Minimum Tilt Angle (degrees) | |
| Maximum Tilt Angle (degrees) | |
| Nominal CS | |
| 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 | Topaz | 0.2.4 |
| PARTICLE SELECTION | cryoSPARC | 3.3.1 |
| IMAGE ACQUISITION | EPU | |
| CTF CORRECTION | cryoSPARC | 3.3.1 |
| MODEL FITTING | Coot | 0.9.8.93 |
| MODEL FITTING | ISOLDE | 1.3 |
| MODEL REFINEMENT | PHENIX | 1.21.1_5286 |
| INITIAL EULER ASSIGNMENT | cryoSPARC | 3.3.1 |
| FINAL EULER ASSIGNMENT | cryoSPARC | 3.3.1 |
| CLASSIFICATION | cryoSPARC | 3.3.1 |
| RECONSTRUCTION | cryoSPARC | 3.3.1 |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING AND AMPLITUDE CORRECTION | Patch CTF in cryoSPARC | 1090375 | Blob picked particles from a subset of micrographs were used to train a TOPAZ model for picking | |
