6T63
A model of the EIAV CA-SP hexamer (C2) from Gag-deltaMA tubes assembled at pH6
ELECTRON MICROSCOPY
| Sample |
|---|
| Equine infectious anemia virus |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | PARTICLE |
| Vitrification Instrument | FEI VITROBOT MARK II |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | 1-2 seconds blot time, offset -3mm |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SUBTOMOGRAM AVERAGING |
| Number of Particles | 112929 |
| Reported Resolution (Å) | 3.8 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | |
| Refinement Type | |
| Symmetry Type | POINT |
| Point Symmetry | C2 |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 (2EIA) | ||||
| Refinement Space | REAL | ||||
| Refinement Protocol | OTHER | ||||
| Refinement Target | Cross-correlation coefficient | ||||
| Overall B Value | |||||
| Fitting Procedure | |||||
| Details | Rigid body fitting was done in Chimera. Missing residues were built de novo in Coot. Refinement was performed iteratively in Phenix and Coot. | ||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | GATAN K2 QUANTUM (4k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 3.4 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | FEI TITAN KRIOS |
| Minimum Defocus (nm) | -1500 |
| Maximum Defocus (nm) | -3500 |
| Minimum Tilt Angle (degrees) | |
| Maximum Tilt Angle (degrees) | |
| Nominal CS | 2.7 |
| Imaging Mode | BRIGHT FIELD |
| Specimen Holder Model | FEI TITAN KRIOS AUTOGRID HOLDER |
| Nominal Magnification | 130000 |
| Calibrated Magnification | |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 300 |
| Imaging Details | nanoprobe |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| VOLUME SELECTION | MATLAB | |
| IMAGE ACQUISITION | SerialEM | |
| CTF CORRECTION | CTFFIND | 4 |
| CTF CORRECTION | NOVACTF | |
| MODEL FITTING | UCSF Chimera | |
| MODEL FITTING | Coot | |
| FINAL EULER ASSIGNMENT | AV3 | |
| FINAL EULER ASSIGNMENT | TOM Toolbox | |
| RECONSTRUCTION | AV3 | |
| RECONSTRUCTION | TOM Toolbox | |
| MODEL REFINEMENT | PHENIX | |
| MODEL REFINEMENT | Coot | |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING AND AMPLITUDE CORRECTION | CTF-correction was performed using NOVACTF | |||
