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The novel DNA binding mechanism of ridinilazole, a precision Clostridiodes difficile antibiotic
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3U2N
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 287 0.01 M Zinc sulphate heptahydrate 0.1 M MES 6.5 25 % v/v PEG 500 MME
Crystal Properties Matthews coefficient Solvent content 2.14 42.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.576 α = 60.78 b = 40.32 β = 87.31 c = 40.577 γ = 61.62
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER2 XE 16M 2020-11-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.2 30.08 96.4 0.99 5.3 1.7 8926
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.27 0.548 1.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3U2N 2.2 30.1 8514 410 96.4 0.22485 0.22373 0.2281 0.24137 0.2459 RANDOM 38.28
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] -0.01 0.09 -0.08 -0.09 -0.05
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 5.44 r_long_range_B_other 5.231 r_scangle_other 3.926 r_scbond_it 3.396 r_scbond_other 3.22 r_angle_refined_deg 2.266 r_angle_other_deg 0.401 r_chiral_restr 0.168 r_gen_planes_refined 0.014 r_bond_refined_d 0.008
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 5.44 r_long_range_B_other 5.231 r_scangle_other 3.926 r_scbond_it 3.396 r_scbond_other 3.22 r_angle_refined_deg 2.266 r_angle_other_deg 0.401 r_chiral_restr 0.168 r_gen_planes_refined 0.014 r_bond_refined_d 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_dihedral_angle_1_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg 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_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 1362 Solvent Atoms 48 Heterogen Atoms 119
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing