8OZP

In situ subtomogram average of Prototype Foamy Virus Env pentamer of trimers


ELECTRON MICROSCOPY

Refinement

RMS Deviations
KeyRefinement Restraint Deviation
r_scangle_other83.545
r_mcbond_it63.906
r_mcbond_other63.906
r_scbond_it43.508
r_scbond_other43.507
r_dihedral_angle_3_deg16.845
r_dihedral_angle_2_deg11.119
r_dihedral_angle_1_deg7.02
r_angle_refined_deg2.087
r_angle_other_deg1.231
RMS Deviations
KeyRefinement Restraint Deviation
r_scangle_other83.545
r_mcbond_it63.906
r_mcbond_other63.906
r_scbond_it43.508
r_scbond_other43.507
r_dihedral_angle_3_deg16.845
r_dihedral_angle_2_deg11.119
r_dihedral_angle_1_deg7.02
r_angle_refined_deg2.087
r_angle_other_deg1.231
r_chiral_restr0.12
r_gen_planes_other0.024
r_gen_planes_refined0.02
r_bond_refined_d0.014
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_mcangle_it
r_mcangle_other
r_scangle_it
r_long_range_B_refined
r_long_range_B_other
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 MethodSUBTOMOGRAM AVERAGING
Number of Particles2220
Reported Resolution (Å)11.9
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Point SymmetryC5
Map-Model Fitting and Refinement
Id1
Refinement SpaceREAL
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)2.62
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelFEI TITAN KRIOS
Minimum Defocus (nm)2000
Maximum Defocus (nm)4500
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
VOLUME SELECTIONDynamo
IMAGE ACQUISITIONFEI tomography
CTF CORRECTIONGctf
MODEL FITTINGISOLDE
MODEL REFINEMENTREFMAC
FINAL EULER ASSIGNMENTRELION
RECONSTRUCTIONRELION
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION