9F3Q
Poliovirus type 1 (strain Mahoney) stabilised virus-like particle (PV1 SC6b) in complex with GPP3 and GSH.
ELECTRON MICROSCOPY
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1HXS |
Refinement
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 11.3 |
f_angle_d | 0.539 |
f_chiral_restr | 0.046 |
f_plane_restr | 0.005 |
f_bond_d | 0.003 |
Sample |
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Human poliovirus 1 Mahoney |
Specimen Preparation | |
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Sample Aggregation State | PARTICLE |
Vitrification Instrument | FEI VITROBOT MARK IV |
Cryogen Name | ETHANE-PROPANE |
Sample Vitrification Details | 3-4 ul of sample blotted for 3.5 seconds with -15 blot force on FEI Vitrobot mark IV. |
3D Reconstruction | |
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Reconstruction Method | SINGLE PARTICLE |
Number of Particles | 23721 |
Reported Resolution (Å) | 2.75 |
Resolution Method | FSC 0.143 CUT-OFF |
Other Details | Icosahedral symmetry applied to final reconstruction. Final maps were post-processed with an inverse B-factor of -146.7 Angstrom squared. |
Refinement Type | |
Symmetry Type | POINT |
Point Symmetry | I |
Map-Model Fitting and Refinement | |||||
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Id | 1 (1HXS) | ||||
Refinement Space | REAL | ||||
Refinement Protocol | RIGID BODY FIT | ||||
Refinement Target | Cross-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 | FEI FALCON III (4k x 4k) | ||||||||
Electron Dose (electrons/Å**2) | 35.49 |
Imaging Experiment | 1 |
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Date of Experiment | |
Temperature (Kelvin) | |
Microscope Model | FEI TITAN KRIOS |
Minimum Defocus (nm) | 800 |
Maximum Defocus (nm) | 2900 |
Minimum Tilt Angle (degrees) | |
Maximum Tilt Angle (degrees) | |
Nominal CS | 2.7 |
Imaging Mode | DARK FIELD |
Specimen Holder Model | FEI TITAN KRIOS AUTOGRID HOLDER |
Nominal Magnification | 75000 |
Calibrated Magnification | 129629 |
Source | FIELD EMISSION GUN |
Acceleration Voltage (kV) | 300 |
Imaging Details | Calibrated pixel size was 1.08 A/pix. |
EM Software | ||
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Task | Software Package | Version |
PARTICLE SELECTION | cryoSPARC | 4.2.1 |
CTF CORRECTION | cryoSPARC | 4.2.1 |
MODEL FITTING | UCSF Chimera | 1.16 |
MODEL FITTING | Coot | 0.9.6 |
INITIAL EULER ASSIGNMENT | cryoSPARC | 4.2.1 |
FINAL EULER ASSIGNMENT | cryoSPARC | 4.2.1 |
CLASSIFICATION | cryoSPARC | 4.2.1 |
RECONSTRUCTION | cryoSPARC | 4.2.1 |
MODEL REFINEMENT | PHENIX | 1.20.1_4487: |
Image Processing | ||||
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CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
PHASE FLIPPING AND AMPLITUDE CORRECTION | 159830 | Particle picking performed in cryoSPARC using the blob picker. |