9F59 | pdb_00009f59

Poliovirus type 2 (strain MEF-1) stabilised virus-like particle (PV2 SC6b) from a mammalian expression system.

ELECTRON MICROSCOPY

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Starting Model(s)

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

Refinement

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	11.451
f_angle_d	0.502
f_chiral_restr	0.043
f_plane_restr	0.004
f_bond_d	0.002

Sample
Poliovirus 2

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

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	18378
Reported Resolution (Å)	2.3
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 -67.7 Angstrom squared.
Refinement Type
Symmetry Type	POINT
Point Symmetry	I

Map-Model Fitting and Refinement
Id	1 (1EAH)
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.

Data Acquisition
Detector Type	GATAN K2 SUMMIT (4k x 4k)
Electron Dose (electrons/Å**2)	39.08

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
Calibrated Magnification	47393
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details	Preliminary grid screening was performed on a Glacios 200 kV microscope.

EM Software
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_4487-000

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION	CTF correction performed using the Patch CTF job in cryoSPARC.	18864	Particle picking was performed using the template picker in CryoSPARC.