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 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 StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK III
Cryogen NameETHANE
Sample Vitrification Detailsblotting at room temperature with sample at room temperature
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles48271
Reported Resolution (Å)6.9
Resolution MethodFSC 0.5 CUT-OFF
Other DetailsProjection 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 TypePOINT
Point SymmetryD8
Map-Model Fitting and Refinement
Id1
Refinement SpaceREAL
Refinement ProtocolFLEXIBLE FIT
Refinement TargetCross-correlation coefficient
Overall B Value
Fitting Procedure
DetailsMETHOD--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 TypeGENERIC TVIPS (4k x 4k)
Electron Dose (electrons/Å**2)20
Imaging Experiment1
Date of Experiment2009-09-15
Temperature (Kelvin)93
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 Magnification50000
Calibrated Magnification50000
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)160
Imaging Detailsactual magnification at the ccd 87000, camera pixel size 15um, 1.72 angstrom per pixel, data collected semi-automatically with EMTools (TVIPS)
EM Software
TaskSoftware PackageVersion
MODEL FITTINGFlex-EM
MODEL FITTINGMODELLER
MODEL FITTINGUCSF Chimera
RECONSTRUCTIONEMAN2
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
each CCD frame