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High resolution structure of the Streptococcus pneumoniae topoisomerase IV-DNA complex with the novel fluoroquinolone Delafloxacin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3RAE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 300 2.5% Tacsimate,
50 mM Na Cacodylate,
62.5 mM KCl,
7.5 mM MgCl2,
4-7.5% Isopropanol.
30% MPD as cryoprotectant
Crystal Properties Matthews coefficient Solvent content 4.24 71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 157.471 α = 90 b = 157.471 β = 90 c = 212.339 γ = 120
Symmetry Space Group P 31 2 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 EIGER2 XE 16M 2022-10-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.95373 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.393 115.01 96.3 0.564 0.569 0.073 1 8.4 60.8 70836 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.394 2.689 84 4.363 4.483 0.62 0.83 1.8 49.5
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.393 115.01 70682 3458 58.857 0.195 0.1922 0.1937 0.2432 0.2455 51.207
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] -0.489 -0.244 -0.489 1.586
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.252 r_dihedral_angle_6_deg 15.192 r_dihedral_angle_2_deg 8.023 r_dihedral_angle_1_deg 7.653 r_lrange_it 6.982 r_lrange_other 6.972 r_mcangle_it 4.711 r_mcangle_other 4.71 r_scangle_it 4.067 r_scangle_other 4.067
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.252 r_dihedral_angle_6_deg 15.192 r_dihedral_angle_2_deg 8.023 r_dihedral_angle_1_deg 7.653 r_lrange_it 6.982 r_lrange_other 6.972 r_mcangle_it 4.711 r_mcangle_other 4.71 r_scangle_it 4.067 r_scangle_other 4.067 r_mcbond_it 2.83 r_mcbond_other 2.829 r_scbond_it 2.386 r_scbond_other 2.386 r_angle_refined_deg 1.54 r_angle_other_deg 0.477 r_nbd_other 0.231 r_nbd_refined 0.22 r_symmetry_nbd_refined 0.214 r_symmetry_nbd_other 0.196 r_xyhbond_nbd_refined 0.186 r_nbtor_refined 0.182 r_symmetry_xyhbond_nbd_refined 0.163 r_symmetry_nbtor_other 0.079 r_chiral_restr 0.071 r_symmetry_xyhbond_nbd_other 0.03 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11462 Nucleic Acid Atoms 732 Solvent Atoms 418 Heterogen Atoms 92
Software Software Software Name Purpose REFMAC refinement PDB-REDO refinement DIALS data reduction xia2 data reduction Aimless data scaling STARANISO data scaling PHASER phasing