8P13
Cryo-EM structure of Rhodopsin-Gi bound with antibody fragments scFv16 and Fab79, conformation 1
ELECTRON MICROSCOPY
Refinement
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| f_dihedral_angle_d | 8.09 |
| f_angle_d | 1.071 |
| f_chiral_restr | 0.055 |
| f_plane_restr | 0.007 |
| f_bond_d | 0.005 |
| Sample |
|---|
| Rhodopsin-Gi-scFv16-Fab79 complex |
| Sample Components |
| Rhodopsin |
| Guanine nucleotide-binding protein G(i) subunit alpha-1 |
| Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 and Guanine nucleotide-binding protein G(T) subunit gamma-T1 |
| single-chain Fv 16 |
| Immunoglobin G heavy chain FAB fragment and Immunoglobin G light chain |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | PARTICLE |
| Vitrification Instrument | FEI VITROBOT MARK IV |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SINGLE PARTICLE |
| Number of Particles | 98000 |
| Reported Resolution (Å) | 5.2 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | |
| Refinement Type | |
| Symmetry Type | POINT |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 (6FUF, 6QNO, 6QNO, 6QNO, 6QNO, 6CRK) | ||||
| Refinement Space | REAL | ||||
| Refinement Protocol | AB INITIO MODEL | ||||
| Refinement Target | cross-correlation coefficient | ||||
| Overall B Value | 360 | ||||
| Fitting Procedure | |||||
| Details | |||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | GATAN K2 SUMMIT (4k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 60 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | FEI TITAN KRIOS |
| Minimum Defocus (nm) | 800 |
| Maximum Defocus (nm) | 2400 |
| Minimum Tilt Angle (degrees) | |
| Maximum Tilt Angle (degrees) | |
| Nominal CS | |
| Imaging Mode | BRIGHT FIELD |
| Specimen Holder Model | FEI TITAN KRIOS AUTOGRID HOLDER |
| Nominal Magnification | 165000 |
| Calibrated Magnification | |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 300 |
| Imaging Details |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| IMAGE ACQUISITION | EPU | |
| MODEL FITTING | UCSF Chimera | 1.16 |
| MODEL REFINEMENT | PHENIX | 1.20.1-4487 |
| INITIAL EULER ASSIGNMENT | cryoSPARC | 2.13 |
| RECONSTRUCTION | RELION | 3.1 |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING AND AMPLITUDE CORRECTION | 7026029 | |||
