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Cryo-EM structure of the Vibrio natrigens 50S ribosomal subunit in complex with the proline-rich antimicrobial peptide Bac5(1-17).
Refinement RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 19.555 r_long_range_B_other 19.555 r_scangle_other 16.663 r_mcangle_other 15.707 r_mcangle_it 15.705 r_dihedral_angle_3_deg 14.729 r_scbond_it 12.687 r_scbond_other 12.687 r_mcbond_it 12.556 r_mcbond_other 12.556
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 19.555 r_long_range_B_other 19.555 r_scangle_other 16.663 r_mcangle_other 15.707 r_mcangle_it 15.705 r_dihedral_angle_3_deg 14.729 r_scbond_it 12.687 r_scbond_other 12.687 r_mcbond_it 12.556 r_mcbond_other 12.556 r_dihedral_angle_2_deg 12.297 r_dihedral_angle_1_deg 6.819 r_angle_refined_deg 1.422 r_angle_other_deg 0.541 r_chiral_restr 0.063 r_gen_planes_refined 0.016 r_bond_refined_d 0.01 r_gen_planes_other 0.003 r_bond_other_d 0.001 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 Structure of the Proline-rich Antimicrobial Peptide Bac5(1-17) in Complex with the Vibrio natriegens 50S ribosomal subunit
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument Cryogen Name ETHANE-PROPANE Sample Vitrification Details
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 294068 Reported Resolution (Å) 2.7 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT
Map-Model Fitting and Refinement Id 1 Refinement Space Refinement Protocol RIGID BODY FIT Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type FEI FALCON II (4k x 4k) Electron Dose (electrons/Å**2) 1
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model TFS KRIOS Minimum Defocus (nm) 700 Maximum Defocus (nm) 1200 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS Imaging Mode BRIGHT FIELD Specimen Holder Model Nominal Magnification Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version MODEL REFINEMENT REFMAC 5.8.0425
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION