Experiment: 9EYY

 9EYY

Poliovirus type 1 (strain Mahoney) native conformation stabilised virus-like particle (PV1 SC6b) from a yeast 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_d10.551
f_angle_d0.495
f_chiral_restr0.043
f_plane_restr0.004
f_bond_d0.003
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 Particles1320
Reported Resolution (Å)3.3
Resolution MethodFSC 0.143 CUT-OFF
Other DetailsFinal reconstruction was sharpened with Post-processing in RELION using an inverse B-factor of -61.8 Angstroms.
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 TypeGATAN K2 SUMMIT (4k x 4k)
Electron Dose (electrons/Å**2)41.14
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 Magnification130000
Calibrated Magnification47619
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1_4487:
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION4578Particle picking was performed using Xmipp as part of the Scipion software framework.