ELECTRON MICROSCOPY
| Sample |
|---|
| Pentamer of the actinorhodopsin |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | PARTICLE |
| Vitrification Instrument | FEI VITROBOT MARK IV |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | In brief, grids were incubated for 30 seconds, and excess liquid blotted off for 5 seconds applying a blotting force of -6 at 4 degrees and a relative ... |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SINGLE PARTICLE |
| Number of Particles | 184961 |
| Reported Resolution (Å) | 2.84 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | |
| Refinement Type | |
| Symmetry Type | POINT |
| Point Symmetry | C5 |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 | ||||
| Refinement Space | |||||
| Refinement Protocol | |||||
| Refinement Target | |||||
| Overall B Value | |||||
| Fitting Procedure | |||||
| Details | Shiff base bond created between K234 and RETINAL (RET) | ||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | TFS FALCON 4i (4k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 1.01 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | TFS KRIOS |
| Minimum Defocus (nm) | 1000 |
| Maximum Defocus (nm) | 2200 |
| Minimum Tilt Angle (degrees) | |
| Maximum Tilt Angle (degrees) | |
| Nominal CS | 2.7 |
| 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 |
| PARTICLE SELECTION | crYOLO | 1.5 |
| IMAGE ACQUISITION | SerialEM | |
| CTF CORRECTION | Gctf | 1.6 |
| MODEL FITTING | UCSF Chimera | 1.7.1 |
| INITIAL EULER ASSIGNMENT | RELION | 4 |
| FINAL EULER ASSIGNMENT | cryoSPARC | |
| CLASSIFICATION | RELION | 4 |
| RECONSTRUCTION | cryoSPARC | |
| MODEL REFINEMENT | PHENIX | 1.20-4459 |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING AND AMPLITUDE CORRECTION | 431658 | a non-template-driven convolutional neural network (CNN) based-particle picking was performed within CrYOLO (version 1.5). A total of 431,658 particles were selected with the pre-trained general model and extracted from the remaining 8170 dose-weighted micrographs with Relion4 | ||
