S-shaped trans interactions of cadherins model based on fitting C-cadherin (1L3W) to 3D map of desmosomes obtained by electron tomography
ELECTRON MICROSCOPY
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 1L3W | |
| Sample |
|---|
| SKIN |
| Sample Components |
| desmosome |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | TISSUE |
| Vitrification Instrument | |
| Cryogen Name | NITROGEN |
| Sample Vitrification Details | high pressure frozen and freezing substituted with 1% OsO4/0.1% Ur-Ac. in acetone, LX-112 resin embeded sample. 50nm thin section |
| Staining Type | NEGATIVE |
| Staining Material | Osmium tetroxide and Uranyl Acetate |
| Staining Details | |
| Embedding Material | LX-112 resin |
| Embedding Details | |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | TOMOGRAPHY |
| Number of Particles | |
| Reported Resolution (Å) | 30 |
| Resolution Method | |
| Other Details | sectioned sample thickness 47.2 nm, +/- 75 degree dual-axis tilt-series with increment 1 degree dual-axis electron tomography with IMOD. 1.169nm ali ... |
| Refinement Type | |
| Symmetry Type | POINT |
| Point Symmetry | C1 |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 (1L3W) | ||||
| Refinement Space | REAL | ||||
| Refinement Protocol | RIGID BODY FIT | ||||
| Refinement Target | best visual fit using the program AmiraMOL 3.0 | ||||
| Overall B Value | |||||
| Fitting Procedure | |||||
| Details | METHOD--tracking 3D density REFINEMENT PROTOCOL--rigid body | ||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | GENERIC GATAN | ||||||||
| Electron Dose (electrons/Å**2) | 1200 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | 2002-11-23 |
| Temperature (Kelvin) | 295 |
| Microscope Model | FEI/PHILIPS CM200FEG |
| Minimum Defocus (nm) | 300 |
| Maximum Defocus (nm) | 500 |
| Minimum Tilt Angle (degrees) | -78 |
| Maximum Tilt Angle (degrees) | 79 |
| Nominal CS | 2 |
| Imaging Mode | BRIGHT FIELD |
| Specimen Holder Model | |
| Nominal Magnification | 50000 |
| Calibrated Magnification | 68276 |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 200 |
| Imaging Details | Dose is for whole dataset, not individual images |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| RECONSTRUCTION | IMOD | |
| MODEL FITTING | Amira | 3 |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| no CTF correction. Imaging at underfocus 0.4 micron with CM200FEG microscope at 50,000 magnification | ||||
