Structure of Leucine Rich Repeat Kinase 2's ROC domain interacting with the microtubule facing the minus end
ELECTRON MICROSCOPY
| Sample |
|---|
| LRRK2RCKW filament bound to a 11-pf microtubule with MLi-2 present |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | FILAMENT |
| Vitrification Instrument | |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SINGLE PARTICLE |
| Number of Particles | 99854 |
| Reported Resolution (Å) | 5.2 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | Local refinement done on symmetry expanded helical reconstruction. |
| Refinement Type | |
| Symmetry Type | POINT |
| Point Symmetry | C1 |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 | ||||
| Refinement Space | |||||
| Refinement Protocol | FLEXIBLE FIT | ||||
| Refinement Target | |||||
| Overall B Value | |||||
| Fitting Procedure | |||||
| Details | Used AlphaFold model as initial model (Q5S007) using only the ROC domain. TUB1 was added to the initial refinement to prevent ROC model from entering ... | ||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | GATAN K2 SUMMIT (4k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 55 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | FEI TALOS ARCTICA |
| Minimum Defocus (nm) | 1500 |
| Maximum Defocus (nm) | 1500 |
| Minimum Tilt Angle (degrees) | |
| Maximum Tilt Angle (degrees) | |
| Nominal CS | 2.7 |
| Imaging Mode | BRIGHT FIELD |
| Specimen Holder Model | |
| Nominal Magnification | 36000 |
| Calibrated Magnification | |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 200 |
| Imaging Details |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| PARTICLE SELECTION | RELION | |
| IMAGE ACQUISITION | Leginon | |
| CTF CORRECTION | CTFFIND | 4 |
| MODEL FITTING | Rosetta | 3.13 |
| RECONSTRUCTION | cryoSPARC | 3.2 |
| MODEL REFINEMENT | ISOLDE | 1.2.2 |
| MODEL REFINEMENT | Rosetta | 3.13 |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING AND AMPLITUDE CORRECTION | 557577 | Filament Autopicker with templates created by manual picking. This is before symmetry expansion. | ||
