ELECTRON MICROSCOPY

Sample

Active complex of Apaf-1, cytochrome c and pro-caspase 9

Specimen Preperation
Sample Aggregation State PARTICLE
Vitrification Instrument FEI VITROBOT MARK III
Cryogen Name ETHANE
Sample Vitrification Details ?
3D Reconstruction
Reconstruction Method SINGLE PARTICLE
Number of Particles 92867
Reported Resolution (Å) 4.1
Resolution Method FSC 0.143 CUT-OFF
Other Details ?
Refinement Type
Symmetry Type POINT
Map-Model Fitting and Refinement
ID 1
Refinement Space REAL
Refinement Protocol FLEXIBLE FIT
Refinement Target ?
Overall B Value ?
Fitting Procedure ?
Details 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 Type GATAN K2 SUMMIT (4k x 4k)
Electron Dose (electrons/Å2) 1.8
Imaging Experiment
Date of Experiment ?
Temprature (Kelvin)
Microscope Model FEI TITAN KRIOS
Minimum Defocus (nm) 1500
Maximum Defocus (nm) 2400
Minimum Tilt Angle (degrees) ?
Maximum Tilt Angle (degrees) ?
Nominal CS 0.01
Imaging Mode BRIGHT FIELD
Specimen Holder Model FEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification 81000
Calibrated Magnification ?
Source FIELD EMISSION GUN
Acceleration Voltage (kV) 300
Imaging Details data collected with a Cs aberration corrector and a GIF energy filter with a slit width of 20 eV.
Imaging Experiment
Task Software Package Version
PARTICLE SELECTION RELION 1.3
IMAGE ACQUISITION SerialEM ?
CTF CORRECTION CTFFIND4 ?
MODEL FITTING MDFF ?
INITIAL EULER ASSIGNMENT RELION 1.3
FINAL EULER ASSIGNMENT RELION 1.3
CLASSIFICATION RELION 1.4
RECONSTRUCTION RELION 1.4
MODEL REFINEMENT PHENIX ?
Image Processing
CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION ?