☰ Navigation Tabs
High resolution structure of the Streptococcus pneumoniae topoisomerase IV-complex with the V-site 18mer dsDNA and novel fluoroquinolone Delafloxacin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8C41
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 301 2.5% Tacsimate,
50 mM Na Cacodylate,
62.5 mM KCl,
7.5 mM MgCl2,
5.5-7.0% Isopropanol.
30% MPD as cryoprotectant
Crystal Properties Matthews coefficient Solvent content 4.21 71.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 157.14 α = 90 b = 157.14 β = 90 c = 211.636 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 EIGER X 16M 2023-03-09 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 2.402 64.862 96.2 0.341 0.349 0.078 0.997 10.3 20.1 60189
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 2.402 2.891 86.2 2.05 2.102 0.459 0.745 2 20.8
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 2.402 64.862 60017 3063 50.895 0.244 0.2413 0.2413 0.2992 0.2995 26.352
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] -0.546 -0.273 -0.546 1.772
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.89 r_dihedral_angle_6_deg 14.534 r_dihedral_angle_1_deg 8.147 r_dihedral_angle_2_deg 6.664 r_lrange_it 2.356 r_lrange_other 2.353 r_angle_refined_deg 1.382 r_mcangle_it 1.19 r_mcangle_other 1.19 r_scangle_it 0.928
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.89 r_dihedral_angle_6_deg 14.534 r_dihedral_angle_1_deg 8.147 r_dihedral_angle_2_deg 6.664 r_lrange_it 2.356 r_lrange_other 2.353 r_angle_refined_deg 1.382 r_mcangle_it 1.19 r_mcangle_other 1.19 r_scangle_it 0.928 r_scangle_other 0.928 r_mcbond_it 0.705 r_mcbond_other 0.704 r_scbond_it 0.535 r_scbond_other 0.535 r_angle_other_deg 0.449 r_nbd_refined 0.238 r_symmetry_nbd_refined 0.238 r_nbd_other 0.224 r_symmetry_xyhbond_nbd_refined 0.212 r_symmetry_nbd_other 0.202 r_xyhbond_nbd_refined 0.184 r_nbtor_refined 0.183 r_symmetry_nbtor_other 0.08 r_chiral_restr 0.068 r_symmetry_xyhbond_nbd_other 0.022 r_metal_ion_refined 0.01 r_bond_refined_d 0.006 r_gen_planes_refined 0.005 r_bond_other_d 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11512 Nucleic Acid Atoms 732 Solvent Atoms 426 Heterogen Atoms 98
Software Software Software Name Purpose REFMAC refinement PDB-REDO refinement DIALS data scaling xia2 data reduction STARANISO data scaling PHASER phasing