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2.37A structure of gepotidacin with S.aureus DNA gyrase and uncleaved DNA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 6.1 293 1ul preciptant solution and 0.7uls complex microbatch under paraffin oil.
Precipitant is 9% PEG 5000MME, 80mM BisTris pH 6.1. Complex is 0.055mM dimer of S.aureus B27A56 (=0.11mM monomer), 0.16mM duplex DNA (=0.32mM single strand), 60mM Na2SO4, 3mM MnCl2, 18mM Hepes, pH 7.0.
Crystal Properties Matthews coefficient Solvent content 2.65 53.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.341 α = 90 b = 123.653 β = 117.1 c = 94.099 γ = 90
Symmetry Space Group P 1 21 1
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 PILATUS3 S 6M 2015-12-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.97242 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.37 50 99 7.3 7.3 66745
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.37 2.46
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 THROUGHOUT 2.37 49.74 66745 3535 98.23 0.18503 0.1829 0.1829 0.22388 0.224 RANDOM 52.26
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] -23.87 -2.95 47.77 -23.9
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.396 r_dihedral_angle_4_deg 15.881 r_dihedral_angle_3_deg 14.338 r_long_range_B_refined 6.06 r_dihedral_angle_1_deg 5.698 r_mcangle_it 1.585 r_mcbond_it 0.945 r_scbond_it 0.861 r_angle_refined_deg 0.811 r_chiral_restr 0.063
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.396 r_dihedral_angle_4_deg 15.881 r_dihedral_angle_3_deg 14.338 r_long_range_B_refined 6.06 r_dihedral_angle_1_deg 5.698 r_mcangle_it 1.585 r_mcbond_it 0.945 r_scbond_it 0.861 r_angle_refined_deg 0.811 r_chiral_restr 0.063 r_bond_refined_d 0.003 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10289 Nucleic Acid Atoms 785 Solvent Atoms 602 Heterogen Atoms 47
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling REFMAC phasing