8OZK

In situ cryoEM structure of the Prototype Foamy Virus capsid, icosahedral map


ELECTRON MICROSCOPY

Refinement

RMS Deviations
KeyRefinement Restraint Deviation
r_long_range_B_refined51.793
r_long_range_B_other51.792
r_scangle_other44.595
r_mcangle_it37.147
r_mcangle_other37.146
r_scbond_it29.266
r_scbond_other29.264
r_mcbond_it24.871
r_mcbond_other24.867
r_dihedral_angle_3_deg17.119
RMS Deviations
KeyRefinement Restraint Deviation
r_long_range_B_refined51.793
r_long_range_B_other51.792
r_scangle_other44.595
r_mcangle_it37.147
r_mcangle_other37.146
r_scbond_it29.266
r_scbond_other29.264
r_mcbond_it24.871
r_mcbond_other24.867
r_dihedral_angle_3_deg17.119
r_dihedral_angle_1_deg7.025
r_angle_refined_deg1.833
r_dihedral_angle_2_deg1.257
r_angle_other_deg0.9
r_chiral_restr0.067
r_bond_refined_d0.015
r_gen_planes_refined0.006
r_gen_planes_other0.006
r_bond_other_d
r_dihedral_angle_4_deg
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Sample
Eastern chimpanzee simian foamy virus
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK III
Cryogen NameETHANE
Sample Vitrification Details
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles8156
Reported Resolution (Å)3.89
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Point SymmetryI
Map-Model Fitting and Refinement
Id1
Refinement SpaceRECIPROCAL
Refinement ProtocolFLEXIBLE FIT
Refinement Target
Overall B Value
Fitting Procedure
Details
Data Acquisition
Detector TypeGATAN K2 SUMMIT (4k x 4k)
Electron Dose (electrons/Å**2)48
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelFEI TITAN KRIOS
Minimum Defocus (nm)1000
Maximum Defocus (nm)4000
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2.7
Imaging ModeBRIGHT FIELD
Specimen Holder ModelFEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONcrYOLO
IMAGE ACQUISITIONEPU
CTF CORRECTIONGctf
MODEL REFINEMENTREFMAC
INITIAL EULER ASSIGNMENTRELION
FINAL EULER ASSIGNMENTRELION
RECONSTRUCTIONRELION
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION52141