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DNA gyrase complexed with uncleaved DNA and Compound 148 to 1.96 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7MVS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6.2 298 15% PEG 5000 MME, 0.1M Bis-Tris pH 6.2
Crystal Properties Matthews coefficient Solvent content 3 59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.937 α = 90 b = 92.937 β = 90 c = 405.763 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 PILATUS3 6M 2022-12-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97911 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) 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 1.96 30 99.6 0.135 0.049 18.4 8.9 139668
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.96 2 97.1 1.491 0.808
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 1.963 29.697 139668 7060 99.358 0.173 0.1705 0.1749 0.2167 0.2183 50.514
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] -0.03 -0.015 -0.03 0.098
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.963 r_dihedral_angle_3_deg 13.628 r_lrange_it 8.636 r_lrange_other 8.636 r_dihedral_angle_2_deg 8.234 r_scangle_it 7.542 r_scangle_other 7.541 r_dihedral_angle_1_deg 6.342 r_scbond_it 5.248 r_scbond_other 5.248
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.963 r_dihedral_angle_3_deg 13.628 r_lrange_it 8.636 r_lrange_other 8.636 r_dihedral_angle_2_deg 8.234 r_scangle_it 7.542 r_scangle_other 7.541 r_dihedral_angle_1_deg 6.342 r_scbond_it 5.248 r_scbond_other 5.248 r_mcangle_it 4.786 r_mcangle_other 4.786 r_mcbond_it 3.784 r_mcbond_other 3.782 r_angle_refined_deg 1.937 r_angle_other_deg 0.534 r_dihedral_angle_other_2_deg 0.258 r_symmetry_nbd_refined 0.243 r_symmetry_xyhbond_nbd_refined 0.237 r_nbd_refined 0.21 r_symmetry_nbd_other 0.179 r_nbtor_refined 0.179 r_xyhbond_nbd_refined 0.167 r_nbd_other 0.155 r_symmetry_nbtor_other 0.078 r_chiral_restr 0.076 r_symmetry_xyhbond_nbd_other 0.011 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10630 Nucleic Acid Atoms 797 Solvent Atoms 603 Heterogen Atoms 36
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing