5T4D
Cryo-EM structure of Polycystic Kidney Disease protein 2 (PKD2), residues 198-703
ELECTRON MICROSCOPY
Refinement
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| f_dihedral_angle_d | 11.423 |
| f_angle_d | 0.82 |
| f_chiral_restr | 0.049 |
| f_bond_d | 0.011 |
| f_plane_restr | 0.005 |
| Sample |
|---|
| hPKD:198-703 |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | PARTICLE |
| Vitrification Instrument | FEI VITROBOT MARK II |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | blot for 7 seconds, -1 mm offset before plunging |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SINGLE PARTICLE |
| Number of Particles | 93805 |
| Reported Resolution (Å) | 3 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | |
| Refinement Type | |
| Symmetry Type | POINT |
| Point Symmetry | C4 |
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | GATAN K2 SUMMIT (4k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 1.35 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | FEI POLARA 300 |
| Minimum Defocus (nm) | 600 |
| Maximum Defocus (nm) | 2400 |
| Minimum Tilt Angle (degrees) | |
| Maximum Tilt Angle (degrees) | |
| Nominal CS | 2 |
| Imaging Mode | BRIGHT FIELD |
| Specimen Holder Model | |
| Nominal Magnification | 31000 |
| Calibrated Magnification | 41132 |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 300 |
| Imaging Details |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| PARTICLE SELECTION | SamViewer | |
| IMAGE ACQUISITION | UCSFImage4 | |
| CTF CORRECTION | CTFFIND4 | |
| MODEL FITTING | Coot | 0.8.2 |
| INITIAL EULER ASSIGNMENT | RELION | 1.4 |
| FINAL EULER ASSIGNMENT | RELION | 1.4 |
| RECONSTRUCTION | RELION | 1.4 |
| MODEL REFINEMENT | PHENIX | 1.10.1-2155 |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING AND AMPLITUDE CORRECTION | 368032 | semi-automated particle picking | ||
