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--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. | ||||
