5JUY

Active human apoptosome with procaspase-9


ELECTRON MICROSCOPY
Sample
Active complex of Apaf-1, cytochrome c and pro-caspase 9
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK III
Cryogen NameETHANE
Sample Vitrification Details
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles92867
Reported Resolution (Å)4.1
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Point SymmetryC7
Map-Model Fitting and Refinement
Id1
Refinement SpaceREAL
Refinement ProtocolFLEXIBLE FIT
Refinement Target
Overall B Value
Fitting Procedure
DetailsInitial rigid body fitting with Chimera with a previously published starting model (PDB 3J2T), molecular dynamics flexible fitting with MDFF and real ...Initial rigid body fitting with Chimera with a previously published starting model (PDB 3J2T), molecular dynamics flexible fitting with MDFF and real space density refinement with Phenix
Data Acquisition
Detector TypeGATAN K2 SUMMIT (4k x 4k)
Electron Dose (electrons/Å**2)1.8
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelFEI TITAN KRIOS
Minimum Defocus (nm)1500
Maximum Defocus (nm)2400
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS0.01
Imaging ModeBRIGHT FIELD
Specimen Holder ModelFEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification81000
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Detailsdata collected with a Cs aberration corrector and a GIF energy filter with a slit width of 20 eV.
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONRELION1.3
IMAGE ACQUISITIONSerialEM
CTF CORRECTIONCTFFIND4
MODEL FITTINGMDFF
INITIAL EULER ASSIGNMENTRELION1.3
FINAL EULER ASSIGNMENTRELION1.3
CLASSIFICATIONRELION1.4
RECONSTRUCTIONRELION1.4
MODEL REFINEMENTPHENIX
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION