3J31 | pdb_00003j31

Life in the extremes: atomic structure of Sulfolobus Turreted Icosahedral Virus


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2BBD 
experimental modelPDB 4IL7 
Sample
Mature Sulfolobus Turreted Icosahedral Virus
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentHOMEMADE PLUNGER
Cryogen NameETHANE
Sample Vitrification DetailsVitrification carried out at room temperature using liquid ethane and a homemade plunger
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles8903
Reported Resolution (Å)4.5
Resolution MethodFSC 0.143 CUT-OFF
Other DetailsThe final reconstruction was sharpened with a negative temperature factor of 400A2 (Single particle--Applied symmetry: I) Resolution method was FSC a ...The final reconstruction was sharpened with a negative temperature factor of 400A2 (Single particle--Applied symmetry: I) Resolution method was FSC at 0.143 cut-off. The reported resolution is for the entire reconstruction. The resolution of the coat subunit region (B345) is estimated to 3.9 A using the same criterion.
Refinement Type
Symmetry TypePOINT
Point SymmetryI
Map-Model Fitting and Refinement
Id1 (2BBD)2 (4IL7)
Refinement SpaceRECIPROCALRECIPROCAL
Refinement ProtocolFLEXIBLE FITFLEXIBLE FIT
Refinement Target
Overall B Value
Fitting Procedure
DetailsREFINEMENT PROTOCOL--positional (xyz) minimization and isotropic B factor refinement DETAILS--Real space refinement was also carried out using Coot.REFINEMENT PROTOCOL--positional (xyz) minimization and isotropic B factor refinement DETAILS--Real space refinement was also carried out using Coot. ...REFINEMENT PROTOCOL--positional (xyz) minimization and isotropic B factor refinement DETAILS--Real space refinement was also carried out using Coot. Only the N-terminal domain was refined using CNS (residues 3-134). The C-terminal domain (residues 135-222) was only rigid-body fit using Coot and an arbitrary B-factor value of 150 A2 was assigned to it.
Data Acquisition
Detector TypeFEI FALCON I (4k x 4k)
Electron Dose (electrons/Å**2)18
Imaging Experiment1
Date of Experiment2011-03-30
Temperature (Kelvin)90
Microscope ModelFEI TITAN KRIOS
Minimum Defocus (nm)800
Maximum Defocus (nm)2500
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2.7
Imaging ModeBRIGHT FIELD
Specimen Holder ModelFEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification
Calibrated Magnification102189
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging DetailsNanoprobe mode was used.
EM Software
TaskSoftware PackageVersion
MODEL FITTINGCNS
RECONSTRUCTIONFREALIGN
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
Each particle