6Z6W
Poliovirus type 3 (strain Saukett) stabilised virus-like particle (PV3 SC8) from a mammalian expression system.
ELECTRON MICROSCOPY
Refinement
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 15.2326 |
f_angle_d | 0.4381 |
f_chiral_restr | 0.0403 |
f_plane_restr | 0.0038 |
f_bond_d | 0.0021 |
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 |
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 | 9630 |
Reported Resolution (Å) | 3 |
Resolution Method | FSC 0.143 CUT-OFF |
Other Details | Final reconstruction was sharpened with Post-processing in RELION using an inverse B-factor of -82.6 Angstroms. |
Refinement Type | |
Symmetry Type | POINT |
Point Symmetry | I |
Map-Model Fitting and Refinement | |||||
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Id | 1 (5O5B) | ||||
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 the refined in real space using Phenix_real.space.refine. |
Data Acquisition | |||||||||
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Detector Type | GATAN K2 SUMMIT (4k x 4k) | ||||||||
Electron Dose (electrons/Å**2) | 40 |
Imaging Experiment | 1 |
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Date of Experiment | |
Temperature (Kelvin) | |
Microscope Model | FEI POLARA 300 |
Minimum Defocus (nm) | 1500 |
Maximum Defocus (nm) | 3500 |
Minimum Tilt Angle (degrees) | |
Maximum Tilt Angle (degrees) | |
Nominal CS | 2.7 |
Imaging Mode | BRIGHT FIELD |
Specimen Holder Model | GATAN LIQUID NITROGEN |
Nominal Magnification | 160000 |
Calibrated Magnification | 37037 |
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 |
MODEL REFINEMENT | PHENIX | dev-3699 |
INITIAL EULER ASSIGNMENT | RELION | 3.1 |
FINAL EULER ASSIGNMENT | RELION | 3.1 |
CLASSIFICATION | RELION | 3.1 |
RECONSTRUCTION | RELION | 3.1 |
Image Processing | ||||
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CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
PHASE FLIPPING AND AMPLITUDE CORRECTION | 14021 |