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Omadacycline and spectinomycin bound to the 30S ribosomal subunit head
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7K00
Refinement RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.848 r_dihedral_angle_2_deg 11.53 r_long_range_B_refined 6.98 r_long_range_B_other 6.958 r_dihedral_angle_1_deg 6.917 r_mcangle_it 4.018 r_mcangle_other 4.018 r_scangle_other 3.971 r_scbond_it 2.47 r_scbond_other 2.468
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.848 r_dihedral_angle_2_deg 11.53 r_long_range_B_refined 6.98 r_long_range_B_other 6.958 r_dihedral_angle_1_deg 6.917 r_mcangle_it 4.018 r_mcangle_other 4.018 r_scangle_other 3.971 r_scbond_it 2.47 r_scbond_other 2.468 r_mcbond_it 2.443 r_mcbond_other 2.443 r_angle_refined_deg 1.227 r_angle_other_deg 0.48 r_chiral_restr 0.049 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_gen_planes_other 0.002 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 Ribosomal small subunit head
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument Cryogen Name ETHANE Sample Vitrification Details
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 514855 Reported Resolution (Å) 2.06 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT
Map-Model Fitting and Refinement Id 1 (7k00) Refinement Space Refinement Protocol Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type GATAN K2 SUMMIT (4k x 4k) Electron Dose (electrons/Å**2) 44
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) 400 Maximum Defocus (nm) 1600 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 5.8.0415
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION