4V4L | pdb_00004v4l

Structure of the Drosophila apoptosome

ELECTRON MICROSCOPY

Sample
Drosophila apoptosome (double ring)
Sample Components
Apaf-1 related killer DARK

Specimen Preparation
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 r ...	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
Point Symmetry	D8

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 in ...	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/Å**2)	20

Imaging Experiment	1
Date of Experiment	2009-09-15
Temperature (Kelvin)	93
Microscope Model	FEI TECNAI F20
Minimum Defocus (nm)	1500
Maximum Defocus (nm)	3000
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS	2
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)

EM Software
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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.