AP-3 bound to myristoylated Arf1 (Q71L) and LAMPI on a lipid nanodisc; combined map
ELECTRON MICROSCOPY
| Sample |
|---|
| AP-3 bound to myristoylated Arf1 (Q71L) and LAMPI on a lipid nanodisc; combined map |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | PARTICLE |
| Vitrification Instrument | SPOTITON |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | Commercialized version - chameleon |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SINGLE PARTICLE |
| Number of Particles | 176749 |
| Reported Resolution (Å) | 4.5 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | Non-Uniform refinement in cryoSPARC. Map is a composite map of two focused refinements, combined using phenix.combine_focused_maps. |
| Refinement Type | |
| Symmetry Type | POINT |
| Point Symmetry | C1 |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 | ||||
| Refinement Space | REAL | ||||
| Refinement Protocol | RIGID BODY FIT | ||||
| Refinement Target | |||||
| Overall B Value | |||||
| Fitting Procedure | |||||
| Details | |||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | FEI FALCON IV (4k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 53.4 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | FEI TITAN KRIOS |
| Minimum Defocus (nm) | 400 |
| Maximum Defocus (nm) | 1400 |
| 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 | 81000 |
| Calibrated Magnification | |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 300 |
| Imaging Details |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| PARTICLE SELECTION | cryoSPARC | 4.4.1 |
| IMAGE ACQUISITION | Leginon | |
| CTF CORRECTION | cryoSPARC | 4.4.1 |
| MODEL FITTING | UCSF ChimeraX | 1.7.1 |
| INITIAL EULER ASSIGNMENT | cryoSPARC | 4.4.1 |
| FINAL EULER ASSIGNMENT | cryoSPARC | 4.4.1 |
| CLASSIFICATION | cryoSPARC | 4.4.1 |
| RECONSTRUCTION | cryoSPARC | 4.4.1 |
| MODEL REFINEMENT | Rosetta | 3.12 |
| MODEL REFINEMENT | PHENIX | 1.21.1 |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING AND AMPLITUDE CORRECTION | Mixture of blob picker, template picker, crYOLO, and Topaz | |||
