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lambda-shaped TRANS and CIS interactions of cadherins model based on fitting C-cadherin (1L3W) to 3D map of desmosomes obtained by electron tomography
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
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 al ... sectioned sample thickness 47.2 nm; +/- 75 degree dual-axis tilt-series
with increment 1 degree, dual-axis electron
tomography with IMOD. 1.169nm alignment error 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