9EZ0 | pdb_00009ez0

Poliovirus type 1 (strain Mahoney) expanded conformation stabilised virus-like particle (PV1 SC6b) from a yeast expression system.

ELECTRON MICROSCOPY

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1HXS

Refinement

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	10.887
f_angle_d	0.508
f_chiral_restr	0.042
f_bond_d	0.004
f_plane_restr	0.004

Sample
Human poliovirus 1 Mahoney

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	FEI VITROBOT MARK IV
Cryogen Name	ETHANE-PROPANE
Sample Vitrification Details	3-4 ul of sample double blotted for 3.5 seconds with -15 blot force on FEI Vitrobot mark IV.

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	2428
Reported Resolution (Å)	3.3
Resolution Method	FSC 0.143 CUT-OFF
Other Details	Final reconstruction was sharpened with Post-processing in RELION using an inverse B-factor of -76.9 Angstroms.
Refinement Type
Symmetry Type	POINT
Point Symmetry	I

Map-Model Fitting and Refinement
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 phenix_real.space.refine. Model fit was optimised using molecular dynamics flexible fitting using Namdinator software.

Data Acquisition
Detector Type	GATAN K2 SUMMIT (4k x 4k)
Electron Dose (electrons/Å**2)	41.14

Imaging Experiment	1
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	130000
Calibrated Magnification	47619
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details

EM Software
Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.20.1_4487:

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION		4578	Particle picking was performed using Xmipp as part of the Scipion software framework.