Homology model of E3 protein of Venezuelan Equine Encephalitis Virus TC-83 strain fitted with a cryo-EM map
ELECTRON MICROSCOPY
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 3N40 | |
| Sample |
|---|
| Venezuelan Equine Encephalitis Virus TC83 strain E3 protein that is cleaved from p62 protein |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | PARTICLE |
| Vitrification Instrument | FEI VITROBOT MARK I |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | vitrification carried out in Chiu lab, Houston, TX |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SINGLE PARTICLE |
| Number of Particles | 37000 |
| Reported Resolution (Å) | 4.8 |
| Resolution Method | |
| Other Details | After each iteration, the non-icosahedral parts (which included the lipids and the RNA) in the reconstruction were removed by a soft-edged mask derive ... |
| Refinement Type | |
| Symmetry Type | POINT |
| Point Symmetry | I |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 (3N40) | ||||
| Refinement Space | REAL | ||||
| Refinement Protocol | RIGID BODY FIT | ||||
| Refinement Target | |||||
| Overall B Value | |||||
| Fitting Procedure | |||||
| Details | METHOD--rigid-body fitting DETAILS--The E3 homology model was not further refined against the cryo-EM density map due to its less-resolved quality | ||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | GATAN ULTRASCAN 4000 (4k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 18 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | 2008-04-09 |
| Temperature (Kelvin) | 96 |
| Microscope Model | JEOL 3200FSC |
| Minimum Defocus (nm) | 400 |
| Maximum Defocus (nm) | 2500 |
| Minimum Tilt Angle (degrees) | |
| Maximum Tilt Angle (degrees) | |
| Nominal CS | 4.3 |
| Imaging Mode | BRIGHT FIELD |
| Specimen Holder Model | JEOL 3200FSC CRYOHOLDER |
| Nominal Magnification | 100000 |
| Calibrated Magnification | |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 300 |
| Imaging Details | omega energy filter |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| MODEL FITTING | UCSF Chimera | |
| RECONSTRUCTION | EMAN | |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| CTF parameters were determined from particles within each CCD image | ||||
