3JBD | pdb_00003jbd

Complex of poliovirus with VHH PVSP6A

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	2PLV
experimental model	PDB	4BEL
experimental model	PDB	2X1P

Refinement

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	19.07
r_dihedral_angle_3_deg	8.162
r_dihedral_angle_4_deg	6.475
r_angle_refined_deg	1.771
r_dihedral_angle_1_deg	1.522
r_chiral_restr	0.122
r_bond_refined_d	0.008
r_gen_planes_refined	0.003

Sample
Nanobody AB6 in complex with poliovirus P1/Mahoney
Sample Components
Human poliovirus 1
Nanobody PVPS6A

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	HOMEMADE PLUNGER
Cryogen Name	ETHANE
Sample Vitrification Details	Blotted for 2 seconds before plunging into liquid ethane (homemade plunger).

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	57282
Reported Resolution (Å)	4.8
Resolution Method	FSC 0.143 CUT-OFF
Other Details	(Single particle details: The particles were processed using frealign.) (Single particle--Applied symmetry: I)
Refinement Type
Symmetry Type	POINT
Point Symmetry	I

Map-Model Fitting and Refinement
Id	1 (1HXS, 2PLV, 4BEL, 2X1P)
Refinement Space	RECIPROCAL
Refinement Protocol	FLEXIBLE FIT
Refinement Target	Stereochemically restrained maximum likelihood refinement of both Fourier phase and amplitude agreement
Overall B Value
Fitting Procedure
Details	REFINEMENT PROTOCOL--Rigid body with some flexible loops and side chains DETAILS--LSQKAB was applied after each refinement cycle to re-impose exact icosahedral operators and rigid body constraints.

Data Acquisition
Detector Type	GATAN ULTRASCAN 4000 (4k x 4k)
Electron Dose (electrons/Å**2)	25

Imaging Experiment	1
Date of Experiment	2012-10-17
Temperature (Kelvin)
Microscope Model	FEI TITAN KRIOS
Minimum Defocus (nm)	1000
Maximum Defocus (nm)	3000
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS	2.6
Imaging Mode	BRIGHT FIELD
Specimen Holder Model	FEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification	96000
Calibrated Magnification	89232
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	200
Imaging Details

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

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