9F0K

Poliovirus type 1 (strain Mahoney) expanded conformation stabilised virus-like particle (PV1 SC6b) from a mammalian expression system


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1HXS 

Refinement

RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d11.295
f_angle_d0.529
f_chiral_restr0.045
f_bond_d0.005
f_plane_restr0.004
Sample
Human poliovirus 1 Mahoney
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK IV
Cryogen NameETHANE-PROPANE
Sample Vitrification Details3-4 ul of sample double blotted for 3.5 seconds with -15 blot force on FEI Vitrobot mark IV.
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles6252
Reported Resolution (Å)3
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Point SymmetryI
Map-Model Fitting and Refinement
Id1 (1HXS)
Refinement SpaceREAL
Refinement ProtocolRIGID BODY FIT
Refinement TargetCross-correlation coefficient
Overall B Value
Fitting Procedure
DetailsInitial model was rigid body fitted using UCSF chimera and Coot. Global minimization and B-factor refinement was performed in real space using pheni ...
Data Acquisition
Detector TypeFEI FALCON III (4k x 4k)
Electron Dose (electrons/Å**2)33.78
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelFEI TITAN KRIOS
Minimum Defocus (nm)800
Maximum Defocus (nm)2900
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2.7
Imaging ModeDARK FIELD
Specimen Holder ModelFEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification75000
Calibrated Magnification129629
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging DetailsPreliminary grid screening was performed on a Glacios 200 kV microscope.
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONcrYOLO
CTF CORRECTIONRELION3.0.7
MODEL FITTINGUCSF Chimera1.16
MODEL FITTINGCoot0.9.6
INITIAL EULER ASSIGNMENTRELION3.0.7
FINAL EULER ASSIGNMENTRELION3.0.7
CLASSIFICATIONRELION3.0.7
RECONSTRUCTIONRELION3.0.7
MODEL REFINEMENTPHENIX1.20.1_4487:
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTIONCTF correction performed in RELION v3.0.7 using CTFFIND4.7185Particle picking was performed using crYOLO after training the neural network on approx. 100 manually picked particles.