8ANW
Poliovirus type 3 (strain Saukett) stabilised virus-like particle (PV3 SC8).
ELECTRON MICROSCOPY
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 6Z6W |
Refinement
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 11.589 |
f_angle_d | 0.485 |
f_chiral_restr | 0.043 |
f_plane_restr | 0.004 |
f_bond_d | 0.002 |
Sample |
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Human poliovirus 3 |
Specimen Preparation | |
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Sample Aggregation State | PARTICLE |
Vitrification Instrument | FEI VITROBOT MARK IV |
Cryogen Name | ETHANE-PROPANE |
Sample Vitrification Details | Double blotting with 4 ul of sample, followed by 4 second blot, before plunging. |
3D Reconstruction | |
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Reconstruction Method | SINGLE PARTICLE |
Number of Particles | 2712 |
Reported Resolution (Å) | 2.7 |
Resolution Method | FSC 0.143 CUT-OFF |
Other Details | Final reconstruction was sharpened with Post-processing in RELION using an inverse B-factor of -69.1 Angstroms. |
Refinement Type | |
Symmetry Type | POINT |
Point Symmetry | I |
Map-Model Fitting and Refinement | |||||
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Id | 1 (6Z6W) | ||||
Refinement Space | REAL | ||||
Refinement Protocol | RIGID BODY FIT | ||||
Refinement Target | Correlation coefficient | ||||
Overall B Value | |||||
Fitting Procedure | |||||
Details | Initial model was rigid body fitted using UCSF chimera and Coot. Global minimization and B-factor refinement was performed in real space using pheni ... |
Data Acquisition | |||||||||
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Detector Type | GATAN K2 SUMMIT (4k x 4k) | ||||||||
Electron Dose (electrons/Å**2) | 35 |
Imaging Experiment | 1 |
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Date of Experiment | |
Temperature (Kelvin) | |
Microscope Model | FEI TITAN KRIOS |
Minimum Defocus (nm) | 900 |
Maximum Defocus (nm) | 2400 |
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 | 165000 |
Calibrated Magnification | 60975 |
Source | FIELD EMISSION GUN |
Acceleration Voltage (kV) | 300 |
Imaging Details |
EM Software | ||
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Task | Software Package | Version |
PARTICLE SELECTION | crYOLO | 1.5.6 |
IMAGE ACQUISITION | SerialEM | |
CTF CORRECTION | CTFFIND | 4.0 |
MODEL FITTING | UCSF Chimera | 1.14 |
INITIAL EULER ASSIGNMENT | RELION | 3.1.1 |
FINAL EULER ASSIGNMENT | RELION | 3.1.1 |
CLASSIFICATION | RELION | 3.1.1 |
RECONSTRUCTION | RELION | 3.1.1 |
MODEL REFINEMENT | PHENIX | 1.19.2-4158-000 |
Image Processing | ||||
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CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
PHASE FLIPPING AND AMPLITUDE CORRECTION | 10744 |