8A5T
Capsid structure of the L-A helper virus from native viral communities
ELECTRON MICROSCOPY
Sample |
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Saccharomyces cerevisiae virus L-A |
Specimen Preparation | |
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Sample Aggregation State | PARTICLE |
Vitrification Instrument | FEI VITROBOT MARK IV |
Cryogen Name | ETHANE |
Sample Vitrification Details | blot force 2 and blot time 6 s before plunging |
3D Reconstruction | |
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Reconstruction Method | SINGLE PARTICLE |
Number of Particles | 1020420 |
Reported Resolution (Å) | 3.78 |
Resolution Method | FSC 0.143 CUT-OFF |
Other Details | |
Refinement Type | |
Symmetry Type | POINT |
Map-Model Fitting and Refinement | |||||
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Id | 1 (1M1C) | ||||
Refinement Space | REAL | ||||
Refinement Protocol | RIGID BODY FIT | ||||
Refinement Target | |||||
Overall B Value | |||||
Fitting Procedure | |||||
Details | The initial model was rigid-fitted by ChimeraX and refined by iterative cycles of Coot and PHENIX. |
Data Acquisition | |||||||||
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Detector Type | FEI FALCON III (4k x 4k) | ||||||||
Electron Dose (electrons/Å**2) | 30 |
Imaging Experiment | 1 |
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Date of Experiment | |
Temperature (Kelvin) | |
Microscope Model | TFS GLACIOS |
Minimum Defocus (nm) | 1000 |
Maximum Defocus (nm) | 2000 |
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 | 92000 |
Calibrated Magnification | 89297 |
Source | FIELD EMISSION GUN |
Acceleration Voltage (kV) | 200 |
Imaging Details |
EM Software | ||
---|---|---|
Task | Software Package | Version |
PARTICLE SELECTION | cryoSPARC | v3.3 |
IMAGE ACQUISITION | EPU | 2.11.1.11REL |
CTF CORRECTION | cryoSPARC | v.3.3 |
MODEL FITTING | UCSF ChimeraX | 1.3 |
MODEL REFINEMENT | Coot | 0.9.6 |
MODEL REFINEMENT | PHENIX | dev-4379 |
CLASSIFICATION | cryoSPARC | v3.3 |
RECONSTRUCTION | cryoSPARC | v3.3 |
Image Processing | ||||
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CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
NONE | 2725140 |