☰ Navigation Tabs
Experimental localization of metal-binding sites reveals the role of metal ions in the delafloxacin-stabilized Streptococcus pneumoniae topoisomerase IV DNA cleavage complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8QMB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 50 mM sodium cacodylate, 62.5 mM KCl, 7.5 mM MgCl 2 , 2.5% Tacsimate TM
Hampton Research, 5.5-7% isopropanol, pH 6.5. The protein crystals were
cryoprotected with 50 mM sodium cacodylate pH 6.5, 62.5 mM KCl, 7.5 mM MgCl 2 ,
2.5% Tacsimate TM Hampton Research, 1 mM beta-mercaptoethanol and 30% v/v
MPD before being flash-cooled in liquid nitrogen and collected in elliptical polyimide sample
mounts.
Crystal Properties Matthews coefficient Solvent content 4.37 71.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 158.533 α = 90 b = 158.533 β = 90 c = 210.82 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 PILATUS 12M 2023-09-23 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I23 2.75,3.14,3.54,4.35,4.50,5.16 Diamond I23
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.37 210.82 100 0.215 0.027 0.999 11.6 59.4 124385
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.37 2.41 100 5.369 0.796 0.204 45
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 MOLECULAR REPLACEMENT THROUGHOUT 2.62 79.39 62910 1109 69.46 0.18089 0.18041 0.1888 0.2085 0.2092 RANDOM 48.179
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] -1.27 -0.63 -1.27 4.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.274 r_dihedral_angle_3_deg 15.526 r_dihedral_angle_1_deg 7.359 r_long_range_B_refined 5.662 r_long_range_B_other 5.662 r_scangle_other 2.883 r_mcangle_it 2.718 r_mcangle_other 2.716 r_scbond_it 2.022 r_scbond_other 2.022
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.274 r_dihedral_angle_3_deg 15.526 r_dihedral_angle_1_deg 7.359 r_long_range_B_refined 5.662 r_long_range_B_other 5.662 r_scangle_other 2.883 r_mcangle_it 2.718 r_mcangle_other 2.716 r_scbond_it 2.022 r_scbond_other 2.022 r_mcbond_it 1.564 r_mcbond_other 1.564 r_angle_refined_deg 1.44 r_angle_other_deg 0.455 r_chiral_restr 0.061 r_bond_refined_d 0.013 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11504 Nucleic Acid Atoms 732 Solvent Atoms 108 Heterogen Atoms 110
Software Software Software Name Purpose PDB-REDO refinement PHENIX refinement DIALS data reduction xia2.multiplex data scaling DIMPLE phasing STARANISO data scaling Coot model building