6YAH
AP2 in clathrin coats assembled on a membrane containing dileucine- and tyrosine-based cargo peptides
ELECTRON MICROSCOPY
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 1XA7 | |
| Sample |
|---|
| Clathrin/AP2 coat assembled on AP2 membrane. |
| Sample Components |
| AP-2 complex in clathrin coat, subunits alpha-2 and mu |
| AP-2 complex in clathrin coat, subunit beta |
| AP-2 complex in clathrin coat, subunit sigma |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | 3D ARRAY |
| Vitrification Instrument | LEICA EM GP |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | The sample was supplemented with 10 nm nanogold fiducials, and 3 ul of the mixture was backside blotted for 3 seconds. |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SUBTOMOGRAM AVERAGING |
| Number of Particles | 27630 |
| Reported Resolution (Å) | 10.2 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | |
| Refinement Type | |
| Symmetry Type | POINT |
| Point Symmetry | C1 |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 (1XA7) | ||||
| Refinement Space | REAL | ||||
| Refinement Protocol | FLEXIBLE FIT | ||||
| Refinement Target | correlation coefficient | ||||
| Overall B Value | |||||
| Fitting Procedure | |||||
| Details | |||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | GATAN K2 QUANTUM (4k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 3.2 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | FEI TITAN KRIOS |
| Minimum Defocus (nm) | 1500 |
| Maximum Defocus (nm) | 6500 |
| 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 | 81000 |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 300 |
| Imaging Details |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| IMAGE ACQUISITION | SerialEM | 3.6 |
| CTF CORRECTION | NOVACTF | 1.0 |
| MODEL FITTING | MDFF | 1.7 |
| FINAL EULER ASSIGNMENT | TOM | |
| FINAL EULER ASSIGNMENT | AV3 | |
| CLASSIFICATION | PEET | |
| CLASSIFICATION | Dynamo | |
| RECONSTRUCTION | TOM | |
| RECONSTRUCTION | AV3 | |
| MODEL REFINEMENT | PHENIX | |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING AND AMPLITUDE CORRECTION | CTF correction in novaCTF with by multiplication | |||
