3J9S
Single particle cryo-EM structure of rotavirus VP6 at 2.6 Angstrom resolution
ELECTRON MICROSCOPY
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1QHD |
Sample |
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Bovine rotavirus VP6 |
Specimen Preparation | |
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Sample Aggregation State | PARTICLE |
Vitrification Instrument | FEI VITROBOT MARK II |
Cryogen Name | ETHANE |
Sample Vitrification Details | Blot for 4-6 seconds before plunging into liquid ethane (FEI VITROBOT MARK II). |
3D Reconstruction | |
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Reconstruction Method | SINGLE PARTICLE |
Number of Particles | 4000 |
Reported Resolution (Å) | 2.6 |
Resolution Method | FSC 0.143 CUT-OFF |
Other Details | Final map is a 13-fold average of VP6 trimers from the asymmetric unit of the reconstruction of the whole capsid. Data at resolutions higher than 15A ... |
Refinement Type | |
Symmetry Type | POINT |
Point Symmetry | I |
Map-Model Fitting and Refinement | |||||
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Id | 1 (1QHD) | ||||
Refinement Space | REAL | ||||
Refinement Protocol | FLEXIBLE FIT | ||||
Refinement Target | |||||
Overall B Value | |||||
Fitting Procedure | |||||
Details | REFINEMENT PROTOCOL--flexible DETAILS--Model was refined by real space refinement using COOT and all restraints. |
Data Acquisition | |||||||||
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Detector Type | GATAN K2 (4k x 4k) | ||||||||
Electron Dose (electrons/Å**2) | 100 |
Imaging Experiment | 1 |
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Date of Experiment | 2014-08-13 |
Temperature (Kelvin) | |
Microscope Model | FEI TITAN KRIOS |
Minimum Defocus (nm) | 400 |
Maximum Defocus (nm) | 2000 |
Minimum Tilt Angle (degrees) | |
Maximum Tilt Angle (degrees) | |
Nominal CS | 2.7 |
Imaging Mode | BRIGHT FIELD |
Specimen Holder Model | |
Nominal Magnification | 29000 |
Calibrated Magnification | |
Source | FIELD EMISSION GUN |
Acceleration Voltage (kV) | 300 |
Imaging Details |
EM Software | ||
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Task | Software Package | Version |
MODEL FITTING | Coot | |
MODEL FITTING | Coot | |
RECONSTRUCTION | FREALIGN | |
RECONSTRUCTION | IMAGIC | |
RECONSTRUCTION | TIGRIS |
Image Processing | ||||
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CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
each particle |