3J0G
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) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3N40 |
Sample |
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Venezuelan Equine Encephalitis Virus TC83 strain E3 protein that is cleaved from p62 protein |
Specimen Preparation | |
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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 | |
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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 | |||||
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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 | |||||||||
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Detector Type | GATAN ULTRASCAN 4000 (4k x 4k) | ||||||||
Electron Dose (electrons/Å**2) | 18 |
Imaging Experiment | 1 |
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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 | ||
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Task | Software Package | Version |
MODEL FITTING | UCSF Chimera | |
RECONSTRUCTION | EMAN |
Image Processing | ||||
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CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
CTF parameters were determined from particles within each CCD image |