5IRZ
Structure of TRPV1 determined in lipid nanodisc
ELECTRON MICROSCOPY
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 3J5P | |
Refinement
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| f_dihedral_angle_d | 9.837 |
| f_angle_d | 0.913 |
| f_chiral_restr | 0.056 |
| f_bond_d | 0.008 |
| f_plane_restr | 0.005 |
| Sample |
|---|
| TRPV1 ion channel in unliganded state |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | PARTICLE |
| Vitrification Instrument | FEI VITROBOT MARK III |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | Blot for 6 seconds before plunging into liquid ethane (FEI VITROBOT MARK III). |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SINGLE PARTICLE |
| Number of Particles | 30689 |
| Reported Resolution (Å) | 3.28 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | |
| Refinement Type | |
| Symmetry Type | POINT |
| Point Symmetry | C4 |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 (3J5P) | ||||
| Refinement Space | REAL | ||||
| Refinement Protocol | RIGID BODY FIT | ||||
| Refinement Target | correlation coefficient | ||||
| Overall B Value | |||||
| Fitting Procedure | |||||
| Details | |||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | GATAN K2 SUMMIT (4k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 41 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | FEI POLARA 300 |
| Minimum Defocus (nm) | 700 |
| Maximum Defocus (nm) | 2200 |
| Minimum Tilt Angle (degrees) | |
| Maximum Tilt Angle (degrees) | |
| Nominal CS | 2 |
| Imaging Mode | BRIGHT FIELD |
| Specimen Holder Model | OTHER |
| Nominal Magnification | 31000 |
| Calibrated Magnification | 41132 |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 300 |
| Imaging Details | Grid screening was performed manually. |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| PARTICLE SELECTION | SPIDER | |
| IMAGE ACQUISITION | UCSFImage4 | |
| CTF CORRECTION | CTFFIND4 | 4 |
| MODEL FITTING | UCSF Chimera | 1.10 |
| INITIAL EULER ASSIGNMENT | RELION | 1.3 |
| FINAL EULER ASSIGNMENT | RELION | 1.3 |
| CLASSIFICATION | RELION | 1.3 |
| RECONSTRUCTION | RELION | 1.3 |
| MODEL REFINEMENT | Coot | |
| MODEL REFINEMENT | PHENIX | |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING AND AMPLITUDE CORRECTION | CTF correction was performed before classification and refinement. | 159193 | Initial manual particle picking and automatic particle picking were performed using SamViewer and several python scripts based on SPIDER. | |
