3J8F | pdb_00003j8f

Cryo-EM reconstruction of poliovirus-receptor complex

ELECTRON MICROSCOPY

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1HXS
experimental model	PDB	4FQP

Refinement

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	5.397
r_dihedral_angle_3_deg	2.307
r_angle_refined_deg	2.032
r_dihedral_angle_4_deg	1.866
r_dihedral_angle_1_deg	0.335
r_chiral_restr	0.154
r_bond_refined_d	0.01
r_gen_planes_refined	0.002

Sample
Type I poliovirus (Mahoney) in complex with enzymatically deglycosylated 3-ecto-domain receptor (PVR, CD155)
Sample Components
Human poliovirus 1 Mahoney
Poliovirus receptor

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	HOMEMADE PLUNGER
Cryogen Name	ETHANE
Sample Vitrification Details	Sample mixed and frozen within 2 minutes before plunging into liquid ethane.

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	9248
Reported Resolution (Å)	4
Resolution Method	FSC 0.143 CUT-OFF
Other Details	(Single particle--Applied symmetry: I)
Refinement Type
Symmetry Type	POINT
Point Symmetry	I

Map-Model Fitting and Refinement
Id	1 (1HXS, 1HXS, 1HXS, 1HXS, 4FQP)
Refinement Space	RECIPROCAL
Refinement Protocol	FLEXIBLE FIT
Refinement Target	pseudo-real space
Overall B Value
Fitting Procedure
Details	REFINEMENT PROTOCOL--flexible DETAILS--After rigid-body fitting, manual rebuilding of the model was alternated with automated stereochemically restrained refinement, minimizing the discrepancy between the experimental and model-based Fourier amplitudes and phases.

Data Acquisition
Detector Type	GATAN K2 (4k x 4k)
Electron Dose (electrons/Å**2)	25

Imaging Experiment	1
Date of Experiment	2013-11-01
Temperature (Kelvin)	100
Microscope Model	FEI POLARA 300
Minimum Defocus (nm)	1000
Maximum Defocus (nm)	3000
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS	2.26
Imaging Mode	BRIGHT FIELD
Specimen Holder Model	OTHER
Nominal Magnification	27500
Calibrated Magnification	25355
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details	K2 Summit super-resolution mode used

EM Software
Task	Software Package	Version
MODEL FITTING	Coot
MODEL FITTING	REFMAC	5
MODEL FITTING	SPDBV
RECONSTRUCTION	FREALIGN
RECONSTRUCTION	RELION	1.2

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
	per micrograph