5K47
CryoEM structure of the human Polycystin-2/PKD2 TRP channel
ELECTRON MICROSCOPY
Refinement
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 30.759 |
| r_dihedral_angle_4_deg | 15.678 |
| r_dihedral_angle_3_deg | 13.272 |
| r_long_range_B_refined | 12.001 |
| r_long_range_B_other | 12 |
| r_mcangle_other | 7.749 |
| r_mcangle_it | 7.748 |
| r_scangle_other | 6.486 |
| r_dihedral_angle_1_deg | 5.875 |
| r_mcbond_it | 4.266 |
| Sample |
|---|
| Polycystin-2 channel tetramer (residues 185-723) |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | PARTICLE |
| Vitrification Instrument | FEI VITROBOT MARK IV |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | 3 microlitres were applied to the grid and blotted for 3secs prior to plunge in liquid ethane |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SINGLE PARTICLE |
| Number of Particles | 19546 |
| Reported Resolution (Å) | 4.22 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | Resolution determined by gold-standard FSC procedure as implemented in RELION |
| Refinement Type | |
| Symmetry Type | POINT |
| Point Symmetry | C4 |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 | ||||
| Refinement Space | RECIPROCAL | ||||
| Refinement Protocol | AB INITIO MODEL | ||||
| Refinement Target | |||||
| Overall B Value | |||||
| Fitting Procedure | |||||
| Details | Model was built directly into map de novo | ||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | GATAN K2 SUMMIT (4k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 45.1 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | FEI POLARA 300 |
| Minimum Defocus (nm) | 1100 |
| Maximum Defocus (nm) | 4500 |
| Minimum Tilt Angle (degrees) | |
| Maximum Tilt Angle (degrees) | |
| Nominal CS | 2 |
| Imaging Mode | BRIGHT FIELD |
| Specimen Holder Model | SIDE ENTRY, EUCENTRIC |
| Nominal Magnification | 37037 |
| Calibrated Magnification | |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 300 |
| Imaging Details |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| PARTICLE SELECTION | RELION | 1.3 |
| IMAGE ACQUISITION | SerialEM | |
| CTF CORRECTION | CTFFIND | 4.0.8 |
| CTF CORRECTION | RELION | 1.3 |
| MODEL FITTING | Coot | |
| MODEL REFINEMENT | REFMAC | 5.8.0135 |
| INITIAL EULER ASSIGNMENT | RELION | 1.3 |
| FINAL EULER ASSIGNMENT | RELION | 1.3 |
| CLASSIFICATION | RELION | 1.3 |
| RECONSTRUCTION | RELION | 1.3 |
| MODEL REFINEMENT | RELION | 1.3 |
| MODEL REFINEMENT | CTFFIND | 4 |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING AND AMPLITUDE CORRECTION | CTF correction as implemented in CTTFIND4/RELION | 161965 | Particles were autopicked using CTF-corrected template based picking algorithm in RELION using selected 2D class averages based on manually picked particles. | |
