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2.8A STRUCTURE OF ZOLIFLODACIN WITH S.AUREUS DNA GYRASE AND DNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5CDM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 6.3 293 90 mM bistris pH 6.3, 9% PEG 5000MME
Crystal Properties Matthews coefficient Solvent content 3.28 62.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.542 α = 90 b = 94.542 β = 90 c = 417.134 γ = 120
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 S 9M 2022-08-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.9999 Diamond I24
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 2.78 25 100 0.997 5.9 18.5 52704
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 2.78 2.83 0.318
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT 5CDM 2.8 24.854 51323 2538 99.405 0.193 0.1908 0.1886 0.2314 0.2302 92.396
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] 2.23 1.115 2.23 -7.233
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.114 r_dihedral_angle_4_deg 17.035 r_dihedral_angle_3_deg 16.392 r_lrange_it 12.356 r_dihedral_angle_1_deg 5.768 r_scangle_it 4.387 r_mcangle_it 3.131 r_scbond_it 2.739 r_mcbond_it 1.817 r_angle_refined_deg 1.722
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.114 r_dihedral_angle_4_deg 17.035 r_dihedral_angle_3_deg 16.392 r_lrange_it 12.356 r_dihedral_angle_1_deg 5.768 r_scangle_it 4.387 r_mcangle_it 3.131 r_scbond_it 2.739 r_mcbond_it 1.817 r_angle_refined_deg 1.722 r_nbtor_refined 0.32 r_symmetry_nbd_refined 0.253 r_nbd_refined 0.221 r_xyhbond_nbd_refined 0.18 r_symmetry_xyhbond_nbd_refined 0.167 r_chiral_restr 0.114 r_bond_refined_d 0.009 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10545 Nucleic Acid Atoms 801 Solvent Atoms 227 Heterogen Atoms 130
Software Software Software Name Purpose REFMAC refinement DIALS data reduction DIALS data scaling PHENIX phasing