6T61
A model of the EIAV CA-SP hexamer (C2) from Gag-deltaMA tubes assembled at pH8
ELECTRON MICROSCOPY
Sample |
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Equine infectious anemia virus |
Specimen Preparation | |
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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 | |
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Reconstruction Method | SUBTOMOGRAM AVERAGING |
Number of Particles | 89860 |
Reported Resolution (Å) | 3.7 |
Resolution Method | FSC 0.143 CUT-OFF |
Other Details | |
Refinement Type | |
Symmetry Type | POINT |
Point Symmetry | C2 |
Map-Model Fitting and Refinement | |||||
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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 | |||||||||
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Detector Type | GATAN K2 QUANTUM (4k x 4k) | ||||||||
Electron Dose (electrons/Å**2) | 3.4 |
Imaging Experiment | 1 |
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Date of Experiment | |
Temperature (Kelvin) | |
Microscope Model | FEI TITAN KRIOS |
Minimum Defocus (nm) | -1500 |
Maximum Defocus (nm) | -5000 |
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 | 105000 |
Calibrated Magnification | |
Source | FIELD EMISSION GUN |
Acceleration Voltage (kV) | 300 |
Imaging Details | Nanoprobe |
EM Software | ||
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Task | Software Package | Version |
VOLUME SELECTION | MATLAB | |
IMAGE ACQUISITION | SerialEM | |
CTF CORRECTION | CTFFIND | 4 |
CTF CORRECTION | CTFPHASEFLIP | |
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 | ||||
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CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
PHASE FLIPPING AND AMPLITUDE CORRECTION | CTF-correction was initially performed using ctfphaseflip in IMOD and NovaCTF in the final steps |