Experiment: 3JBE

ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4IOC

Refinement

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	6.172
r_dihedral_angle_3_deg	2.705
r_angle_refined_deg	2.346
r_dihedral_angle_4_deg	1.957
r_dihedral_angle_1_deg	0.38
r_chiral_restr	0.19
r_bond_refined_d	0.012
r_gen_planes_refined	0.002

Sample
Nanobody PVSS8A in complex with poliovirus P1/Mahoney
Sample Components
Human poliovirus 1
PVSS8A

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	HOMEMADE PLUNGER
Cryogen Name	ETHANE
Sample Vitrification Details	Blotted for 4 seconds before plunging into liquid ethane (homemade plunger).

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	16421
Reported Resolution (Å)	4.2
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 (4IOC)
Refinement Space	RECIPROCAL
Refinement Protocol	FLEXIBLE FIT
Refinement Target	ML agreement with Fourier amplitudes and phases
Overall B Value
Fitting Procedure
Details	REFINEMENT PROTOCOL--flexible DETAILS--Using stereochemically and icosahedrally restrained maximum likelihood refinement in REFMAC5, a representative ...	REFINEMENT PROTOCOL--flexible DETAILS--Using stereochemically and icosahedrally restrained maximum likelihood refinement in REFMAC5, a representative subset of the full atomic model with all neighbors present was built and refined to fit the corresponding subset of the experimental map. Portions of the model whose density resembled a structural homolog were identified and restrained to agree with the homolog. Detailed atomic models were constructed in areas of difference wherever the resolution of the map permitted. The Fourier-amplitude-weighted average cosine of the phase discrepancy was tracked.

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

Imaging Experiment	1
Date of Experiment	2013-11-27
Temperature (Kelvin)	80
Microscope Model	FEI POLARA 300
Minimum Defocus (nm)	-1400
Maximum Defocus (nm)	-4000
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS	2.26
Imaging Mode	BRIGHT FIELD
Specimen Holder Model	OTHER
Nominal Magnification	23000
Calibrated Magnification	25381
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details	Gatan K2 operated in Super-resolution mode

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.