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Structure of major capsid protein VP1 of Aeropyrum pernix bacilliform virus 1 APBV1
Refinement RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.726 r_dihedral_angle_3_deg 24.644 r_long_range_B_refined 22.829 r_long_range_B_other 22.828 r_scangle_other 19.055 r_dihedral_angle_4_deg 15.731 r_mcangle_it 13.873 r_mcangle_other 13.872 r_scbond_it 11.654 r_scbond_other 11.65
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.726 r_dihedral_angle_3_deg 24.644 r_long_range_B_refined 22.829 r_long_range_B_other 22.828 r_scangle_other 19.055 r_dihedral_angle_4_deg 15.731 r_mcangle_it 13.873 r_mcangle_other 13.872 r_scbond_it 11.654 r_scbond_other 11.65 r_mcbond_it 8.228 r_mcbond_other 8.226 r_dihedral_angle_1_deg 7.011 r_angle_other_deg 3.742 r_angle_refined_deg 1.984 r_chiral_restr 0.123 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 r_gen_planes_other 0.006 r_bond_other_d 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 Aeropyrum pernix bacilliform virus 1
Specimen Preparation Sample Aggregation State HELICAL ARRAY Vitrification Instrument Cryogen Name ETHANE-PROPANE Sample Vitrification Details
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 94645 Reported Resolution (Å) 3.7 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C5
Map-Model Fitting and Refinement Id 1 Refinement Space Refinement Protocol AB INITIO MODEL Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type GATAN K2 QUANTUM (4k x 4k) Electron Dose (electrons/Å**2) 1
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI POLARA 300 Minimum Defocus (nm) Maximum Defocus (nm) Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS 2 Imaging Mode BRIGHT FIELD Specimen Holder Model Nominal Magnification Calibrated Magnification 37037 Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version IMAGE ACQUISITION SerialEM CTF CORRECTION CTFFIND 3 MODEL FITTING Coot INITIAL EULER ASSIGNMENT SPRING FINAL EULER ASSIGNMENT SPRING RECONSTRUCTION SPRING MODEL REFINEMENT REFMAC MODEL REFINEMENT PHENIX
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 169316 Overlapping segments extracted from helical particles