ELECTRON MICROSCOPY

Sample

Human Apaf-1 apoptosome with stably bound cytochrome c and procaspase-9 CARDs.

Specimen Preperation
Sample Aggregation State PARTICLE
Vitrification Instrument FEI VITROBOT MARK III
Cryogen Name ETHANE
Sample Vitrification Details Blot for 2 seconds before plunging (FEI VITROBOT MARK III)
3D Reconstruction
Reconstruction Method SINGLE PARTICLE
Number of Particles 34000
Reported Resolution (Å) 9.5
Resolution Method ?
Other Details EMAN was used for reconstruction using C7 symmetry.
Refinement Type
Symmetry Type POINT
Map-Model Fitting and Refinement
ID 1
Refinement Space REAL
Refinement Protocol FLEXIBLE FIT
Refinement Target Cross-correlation coefficient
Overall B Value ?
Fitting Procedure ?
Details METHOD--flexible fitting REFINEMENT PROTOCOL--Rigid body docking followed by flexible fitting DETAILS--Modeller was used to create a full length human Apaf-1. Initial fit was done using Chimera rigid body fitting. Rosetta was used for flexible fitting.
Data Acquisition
Detector Type KODAK SO-163 FILM
Electron Dose (electrons/Å2) 25
Imaging Experiment
Date of Experiment 2008-08-01
Temprature (Kelvin)
Microscope Model FEI TECNAI F20
Minimum Defocus (nm) 1500
Maximum Defocus (nm) 3000
Minimum Tilt Angle (degrees) 0
Maximum Tilt Angle (degrees) 0
Nominal CS 2.0
Imaging Mode BRIGHT FIELD
Specimen Holder Model GATAN LIQUID NITROGEN
Nominal Magnification 62000
Calibrated Magnification 62000
Source FIELD EMISSION GUN
Acceleration Voltage (kV) 120
Imaging Details ?
Imaging Experiment
Task Software Package Version
MODEL FITTING Rosetta ?
MODEL FITTING Situs ?
MODEL FITTING UCSF Chimera ?
RECONSTRUCTION EMAN ?
Image Processing
CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details
. CTF correction was done on each particle image based on summed power spectra from each micrograph.