3J2T

An improved model of the human apoptosome

ELECTRON MICROSCOPY

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

Specimen Preparation
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
Point Symmetry	C7

Map-Model Fitting and Refinement
Id	1 (1Z6T, 3SFZ)	2 (2B4Z)
Refinement Space	REAL	REAL
Refinement Protocol	FLEXIBLE FIT	RIGID BODY FIT
Refinement Target	Cross-correlation coefficient	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 huma ...	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.	METHOD--rigid body fitting REFINEMENT PROTOCOL--rigid body DETAILS--Cytochrome c was fitted into its local density using Situs.

Data Acquisition
Detector Type	KODAK SO-163 FILM
Electron Dose (electrons/Å**2)	25

Imaging Experiment	1
Date of Experiment	2008-08-01
Temperature (Kelvin)	96
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	62000
Calibrated Magnification	62000
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	120
Imaging Details

EM Software
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.

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.