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A 2.58A crystal structure of S. aureus DNA gyrase and DNA with metals identified through anomalous scattering
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5CDR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 6.1 293.15 PEG 5000 MME, 150 mM BisTris pH 6.1, 20 mM HEPES pH 7.0
Crystal Properties Matthews coefficient Solvent content 3.13 60.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.633 α = 90 b = 93.633 β = 90 c = 410.874 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 80 PIXEL DECTRIS PILATUS 12M 2024-01-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I23 1.8785 Diamond I23
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 2.58 57.72 100 0.231 0.233 0.031 1 22.1 55.4 63516 60.3
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 2.58 2.74 99.1 3.783 3.836 0.619 0.542 31.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.58 57.72 1.94 63403 6287 99.86 0.1522 0.1401 0.1329 0.1997 0.1982
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 16.558 f_angle_d 1.28 f_chiral_restr 0.071 f_plane_restr 0.011 f_bond_d 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10615 Nucleic Acid Atoms 793 Solvent Atoms 337 Heterogen Atoms 58
Software Software Software Name Purpose PHENIX refinement REFMAC refinement XDS data reduction PHASER phasing Aimless data scaling