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 29KH | pdb_000029kh

Outer capsid of the ranavirus Frog Virus 3


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
in silico modelAlphaFold 

Refinement

RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d9.4787
f_angle_d0.4877
f_chiral_restr0.0425
f_bond_d0.0041
f_plane_restr0.0038
Sample
Frog virus 3
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK IV
Cryogen NameETHANE
Sample Vitrification DetailsBlottting Force = 4 Blotting time between 3.5 and 5.5 secs
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles2525
Reported Resolution (Å)3
Resolution MethodFSC 0.143 CUT-OFF
Other DetailsThe number of particles refers to the total number of full icosahedral particles, which underwent Block-based reconstruction. The number of subparticl ...The number of particles refers to the total number of full icosahedral particles, which underwent Block-based reconstruction. The number of subparticles in each of the blocks that make up the composite map varies, depending on classification. 4 blocks were used to build composite map, all with comparable resolutions.
Refinement Type
Symmetry TypePOINT
Point SymmetryC1
Map-Model Fitting and Refinement
Id1
Refinement Space
Refinement Protocol
Refinement Target
Overall B Value
Fitting Procedure
Details
Data Acquisition
Detector TypeFEI FALCON IV (4k x 4k)
Electron Dose (electrons/Å**2)40
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelTFS KRIOS
Minimum Defocus (nm)1000
Maximum Defocus (nm)3000
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
Imaging ModeBRIGHT FIELD
Specimen Holder Model
Nominal Magnification
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONRELION4.0.0
PARTICLE SELECTIONTopaz0.2.5
MODEL REFINEMENTPHENIXdev_6003
RECONSTRUCTIONRELION4.0.0
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION