ELECTRON MICROSCOPY
Refinement
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| f_dihedral_angle_d | 3.8218 |
| f_angle_d | 0.5201 |
| f_chiral_restr | 0.0388 |
| f_plane_restr | 0.0043 |
| f_bond_d | 0.0021 |
| Sample |
|---|
| tetrameric complex of alpha-latrotoxin |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | PARTICLE |
| Vitrification Instrument | FEI VITROBOT MARK II |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SINGLE PARTICLE |
| Number of Particles | 442105 |
| Reported Resolution (Å) | 2.7 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | For the final reconstruction, Multibody-refinement, as implemented in Relion was performed, with a total of 8 independent bodies. |
| Refinement Type | |
| Symmetry Type | POINT |
| Point Symmetry | C1 |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 | ||||
| Refinement Space | REAL | ||||
| Refinement Protocol | AB INITIO MODEL | ||||
| Refinement Target | cross correlation 0.72 | ||||
| Overall B Value | 116 | ||||
| Fitting Procedure | |||||
| Details | An Alphafold2 prediction was initially fit into the reconstructiuon using ChimeraX and then manually refined using Coot and energy minimized using Phe ... | ||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | TFS FALCON 4i (4k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 50 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | FEI TITAN KRIOS |
| Minimum Defocus (nm) | 300 |
| Maximum Defocus (nm) | 1700 |
| 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 | 215000 |
| Calibrated Magnification | |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 300 |
| Imaging Details |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| PARTICLE SELECTION | crYOLO | 1.8.3 |
| IMAGE ACQUISITION | EPU | 3.2.0.4776 |
| CTF CORRECTION | RELION | 4.01 |
| MODEL FITTING | UCSF ChimeraX | 1.7.dev2023 |
| INITIAL EULER ASSIGNMENT | RELION | 4.01 |
| FINAL EULER ASSIGNMENT | RELION | 4.01 |
| CLASSIFICATION | RELION | 4.01 |
| RECONSTRUCTION | RELION | 4.01 |
| MODEL REFINEMENT | Coot | 0.9.8.1 |
| MODEL REFINEMENT | PHENIX | 1.20.1 |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING AND AMPLITUDE CORRECTION | 2436143 | Particles were selected using crYOLO with a generalized picking model, followed by retraining with cleaned particle sets and repicking with a such derived optimized picking model. | ||
