3JBD

Complex of poliovirus with VHH PVSP6A


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1HXS 
experimental modelPDB 2PLV 
experimental modelPDB 4BEL 
experimental modelPDB 2X1P 

Refinement

RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg19.07
r_dihedral_angle_3_deg8.162
r_dihedral_angle_4_deg6.475
r_angle_refined_deg1.771
r_dihedral_angle_1_deg1.522
r_chiral_restr0.122
r_bond_refined_d0.008
r_gen_planes_refined0.003
Sample
Nanobody AB6 in complex with poliovirus P1/Mahoney
Sample Components
Human poliovirus 1
Nanobody PVPS6A
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentHOMEMADE PLUNGER
Cryogen NameETHANE
Sample Vitrification DetailsBlotted for 2 seconds before plunging into liquid ethane (homemade plunger).
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles57282
Reported Resolution (Å)4.8
Resolution MethodFSC 0.143 CUT-OFF
Other Details(Single particle details: The particles were processed using frealign.) (Single particle--Applied symmetry: I)
Refinement Type
Symmetry TypePOINT
Point SymmetryI
Map-Model Fitting and Refinement
Id1 (1HXS, 2PLV, 4BEL, 2X1P)
Refinement SpaceRECIPROCAL
Refinement ProtocolFLEXIBLE FIT
Refinement TargetStereochemically restrained maximum likelihood refinement of both Fourier phase and amplitude agreement
Overall B Value
Fitting Procedure
DetailsREFINEMENT PROTOCOL--Rigid body with some flexible loops and side chains DETAILS--LSQKAB was applied after each refinement cycle to re-impose exact ...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 TypeGATAN ULTRASCAN 4000 (4k x 4k)
Electron Dose (electrons/Å**2)25
Imaging Experiment1
Date of Experiment2012-10-17
Temperature (Kelvin)
Microscope ModelFEI TITAN KRIOS
Minimum Defocus (nm)1000
Maximum Defocus (nm)3000
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2.6
Imaging ModeBRIGHT FIELD
Specimen Holder ModelFEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification96000
Calibrated Magnification89232
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)200
Imaging Details
EM Software
TaskSoftware PackageVersion
MODEL FITTINGCoot
MODEL FITTINGREFMAC5
MODEL FITTINGSPDBV
RECONSTRUCTIONFREALIGN
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
per particle