6WCJ
Asymmetric vertex of the clathrin minicoat cage
ELECTRON MICROSCOPY
Refinement
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| f_dihedral_angle_d | 6.8189 |
| f_angle_d | 0.3393 |
| f_chiral_restr | 0.0328 |
| f_plane_restr | 0.0028 |
| f_bond_d | 0.0012 |
| Sample |
|---|
| Natively assembled clathrin coated vesicles |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | PARTICLE |
| Vitrification Instrument | FEI VITROBOT MARK IV |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SINGLE PARTICLE |
| Number of Particles | 305413 |
| Reported Resolution (Å) | 6.3 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | After the final refinement in cisTEM, half-maps were generated in cisTEM and the FSC was calculated with EMAN FSC tools. |
| Refinement Type | |
| Symmetry Type | POINT |
| Point Symmetry | C1 |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 (6SCT, 6SCT, 6SCT) | 2 (6SCT, 6SCT, 6SCT) | 3 (6SCT, 6SCT, 6SCT, 6SCT, 6SCT, 6SCT, 6SCT, 6SCT, 6SCT, 6SCT, 6SCT, 6SCT, 6SCT, 6SCT, 6SCT) | ||
| Refinement Space | |||||
| Refinement Protocol | AB INITIO MODEL | AB INITIO MODEL | FLEXIBLE FIT | ||
| Refinement Target | |||||
| Overall B Value | |||||
| Fitting Procedure | |||||
| Details | |||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | GATAN K3 (6k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 50 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | FEI TITAN KRIOS |
| Minimum Defocus (nm) | 3000 |
| Maximum Defocus (nm) | 5000 |
| 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 | 35000 |
| Calibrated Magnification | |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 300 |
| Imaging Details |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| PARTICLE SELECTION | RELION | 3 |
| IMAGE ACQUISITION | Leginon | |
| CTF CORRECTION | cisTEM | 1 |
| CTF CORRECTION | CTFFIND | 4 |
| CTF CORRECTION | RELION | 3 |
| MODEL FITTING | Rosetta | |
| INITIAL EULER ASSIGNMENT | cryoSPARC | 2 |
| FINAL EULER ASSIGNMENT | cisTEM | 1 |
| FINAL EULER ASSIGNMENT | RELION | 3 |
| RECONSTRUCTION | cisTEM | 1 |
| MODEL REFINEMENT | PHENIX | |
| MODEL FITTING | Rosetta | |
| MODEL REFINEMENT | PHENIX | |
| MODEL FITTING | Rosetta | |
| MODEL REFINEMENT | PHENIX | |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING AND AMPLITUDE CORRECTION | 360000 | These are subparticle images that were extracted from particle images. Each minicoat particle has 24 asymmetric vertices. From a total of 15000 minicoat particles, 360000 vertex subparticles were extracted. The position of subparticles was calculated by the localized reconstruction script in scipion, and the subparticle images were extracted with RELION extraction tools. | ||
