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 3J2T | pdb_00003j2t

An improved model of the human apoptosome


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1Z6T 
experimental modelPDB 3SFZ 
experimental modelPDB 2B4Z 
Sample
Human Apaf-1 apoptosome with stably bound cytochrome c and procaspase-9 CARDs.
Sample Components
Apaf-1
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK III
Cryogen NameETHANE
Sample Vitrification DetailsBlot for 2 seconds before plunging (FEI VITROBOT MARK III)
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles34000
Reported Resolution (Å)9.5
Resolution Method
Other DetailsEMAN was used for reconstruction using C7 symmetry.
Refinement Type
Symmetry TypePOINT
Point SymmetryC7
Map-Model Fitting and Refinement
Id1 (1Z6T, 3SFZ)2 (2B4Z)
Refinement SpaceREALREAL
Refinement ProtocolFLEXIBLE FITRIGID BODY FIT
Refinement TargetCross-correlation coefficientCross-correlation coefficient
Overall B Value
Fitting Procedure
DetailsMETHOD--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 TypeKODAK SO-163 FILM
Electron Dose (electrons/Å**2)25
Imaging Experiment1
Date of Experiment2008-08-01
Temperature (Kelvin)96
Microscope ModelFEI TECNAI F20
Minimum Defocus (nm)1500
Maximum Defocus (nm)3000
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2
Imaging ModeBRIGHT FIELD
Specimen Holder ModelGATAN LIQUID NITROGEN
Nominal Magnification62000
Calibrated Magnification62000
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)120
Imaging Details
EM Software
TaskSoftware PackageVersion
MODEL FITTINGRosetta
MODEL FITTINGSitus
MODEL FITTINGUCSF Chimera
RECONSTRUCTIONEMAN
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
CTF correction was done on each particle image based on summed power spectra from each micrograph.