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In situ cryoEM structure of the Prototype Foamy Virus capsid, icosahedral map
Refinement RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 51.793 r_long_range_B_other 51.792 r_scangle_other 44.595 r_mcangle_it 37.147 r_mcangle_other 37.146 r_scbond_it 29.266 r_scbond_other 29.264 r_mcbond_it 24.871 r_mcbond_other 24.867 r_dihedral_angle_3_deg 17.119
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 51.793 r_long_range_B_other 51.792 r_scangle_other 44.595 r_mcangle_it 37.147 r_mcangle_other 37.146 r_scbond_it 29.266 r_scbond_other 29.264 r_mcbond_it 24.871 r_mcbond_other 24.867 r_dihedral_angle_3_deg 17.119 r_dihedral_angle_1_deg 7.025 r_angle_refined_deg 1.833 r_dihedral_angle_2_deg 1.257 r_angle_other_deg 0.9 r_chiral_restr 0.067 r_bond_refined_d 0.015 r_gen_planes_refined 0.006 r_gen_planes_other 0.006 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 State PARTICLE Vitrification Instrument FEI VITROBOT MARK III Cryogen Name ETHANE Sample Vitrification Details
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 8156 Reported Resolution (Å) 3.89 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry I
Map-Model Fitting and Refinement Id 1 Refinement Space RECIPROCAL Refinement Protocol FLEXIBLE FIT Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type GATAN K2 SUMMIT (4k x 4k) Electron Dose (electrons/Å**2) 48
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) 1000 Maximum Defocus (nm) 4000 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS 2.7 Imaging Mode BRIGHT FIELD Specimen Holder Model FEI TITAN KRIOS AUTOGRID HOLDER Nominal Magnification Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION crYOLO IMAGE ACQUISITION EPU CTF CORRECTION Gctf MODEL REFINEMENT REFMAC INITIAL EULER ASSIGNMENT RELION FINAL EULER ASSIGNMENT RELION RECONSTRUCTION RELION
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 52141