ELECTRON MICROSCOPY

Sample

Drosophila apoptosome (double ring)

Specimen Preperation
Sample Aggregation State PARTICLE
Vitrification Instrument FEI VITROBOT MARK III
Cryogen Name ETHANE
Sample Vitrification Details blotting at room temperature with sample at room temperature
3D Reconstruction
Reconstruction Method SINGLE PARTICLE
Number of Particles 48271
Reported Resolution (Å) 6.9
Resolution Method FSC 0.5 CUT-OFF
Other Details Projection matching was done with Fourier ring correlation, model-based masking and SSNR weighting over an 80-6 angstrom resolution range. The final refinement steps used an angular step of 2.5 degrees and each of the 48,000 particles was matched to the best two projection classes (1353). In total, 45,000 particles were used in the final reconstruction and the 3D map was amplitude corrected then Gaussian low-pass filtered with a Fourier half-width of 0.12.
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, local refinement REFINEMENT PROTOCOL--rigid body first, and then used individual helices DETAILS--Chimera was used to do initial domain fitting with Apaf-1 (1Z6T) and CED-4 (2A5Y)domains. Modeller and Flex-Em were then used to do local refinement of homology models of the various domains.
Data Acquisition
Detector Type GENERIC TVIPS (4k x 4k)
Electron Dose (electrons/Å2) 20
Imaging Experiment
Date of Experiment 2009-09-15
Temprature (Kelvin)
Microscope Model FEI TECNAI F20
Minimum Defocus (nm) 1500
Maximum Defocus (nm) 3000
Minimum Tilt Angle (degrees) 0.0
Maximum Tilt Angle (degrees) 0.0
Nominal CS 2.0
Imaging Mode BRIGHT FIELD
Specimen Holder Model GATAN LIQUID NITROGEN
Nominal Magnification 50000
Calibrated Magnification 50000
Source FIELD EMISSION GUN
Acceleration Voltage (kV) 160
Imaging Details actual magnification at the ccd 87000, camera pixel size 15um, 1.72 angstrom per pixel, data collected semi-automatically with EMTools (TVIPS)
Imaging Experiment
Task Software Package Version
MODEL FITTING Flex-EM ?
MODEL FITTING MODELLER ?
MODEL FITTING UCSF Chimera ?
RECONSTRUCTION EMAN 2
Image Processing
CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details
. each CCD frame