3KK5
Crystal structure of PBCV-1 VP54 fitted into a cryo-EM reconstruction of the virophage Sputnik
ELECTRON MICROSCOPY
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1M3Y |
Sample |
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major capsid protein of sputnik |
Specimen Preparation | |
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Sample Aggregation State | PARTICLE |
Vitrification Instrument | HOMEMADE PLUNGER |
Cryogen Name | ETHANE |
Sample Vitrification Details | flash-frozen on holey grids in liquid ethane |
3D Reconstruction | |
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Reconstruction Method | SINGLE PARTICLE |
Number of Particles | 6780 |
Reported Resolution (Å) | 10.6 |
Resolution Method | |
Other Details | EMAN |
Refinement Type | |
Symmetry Type | POINT |
Point Symmetry | I |
Map-Model Fitting and Refinement | |||||
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Id | 1 (1M3Y) | ||||
Refinement Space | REAL | ||||
Refinement Protocol | RIGID BODY FIT | ||||
Refinement Target | Sumf | ||||
Overall B Value | |||||
Fitting Procedure | |||||
Details | REFINEMENT PROTOCOL--rigid body |
Data Acquisition | |||||||||
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Detector Type | GENERIC FILM | ||||||||
Electron Dose (electrons/Å**2) | 20 |
Imaging Experiment | 1 |
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Date of Experiment | |
Temperature (Kelvin) | 70 |
Microscope Model | FEI/PHILIPS CM200FEG |
Minimum Defocus (nm) | 767 |
Maximum Defocus (nm) | 3582 |
Minimum Tilt Angle (degrees) | |
Maximum Tilt Angle (degrees) | |
Nominal CS | 2 |
Imaging Mode | BRIGHT FIELD |
Specimen Holder Model | |
Nominal Magnification | 38000 |
Calibrated Magnification | 39190 |
Source | FIELD EMISSION GUN |
Acceleration Voltage (kV) | 200 |
Imaging Details |
EM Software | ||
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Task | Software Package | Version |
MODEL FITTING | EMfit | |
RECONSTRUCTION | EMAN |
Image Processing | ||||
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CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
CTF parameters were calculated for particles in each micrograph. |