9F0K | pdb_00009f0k

Poliovirus type 1 (strain Mahoney) expanded conformation stabilised virus-like particle (PV1 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	1HXS

Refinement

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	11.295
f_angle_d	0.529
f_chiral_restr	0.045
f_bond_d	0.005
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	6252
Reported Resolution (Å)	3
Resolution Method	FSC 0.143 CUT-OFF
Other Details
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.

Data Acquisition
Detector Type	FEI FALCON III (4k x 4k)
Electron Dose (electrons/Å**2)	33.78

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	75000
Calibrated Magnification	129629
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	crYOLO
CTF CORRECTION	RELION	3.0.7
MODEL FITTING	UCSF Chimera	1.16
MODEL FITTING	Coot	0.9.6
INITIAL EULER ASSIGNMENT	RELION	3.0.7
FINAL EULER ASSIGNMENT	RELION	3.0.7
CLASSIFICATION	RELION	3.0.7
RECONSTRUCTION	RELION	3.0.7
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	CTF correction performed in RELION v3.0.7 using CTFFIND4.	7185	Particle picking was performed using crYOLO after training the neural network on approx. 100 manually picked particles.