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Structure of Staphylococcus aureus Y131F DNA gyrase GK-del fusion construct in complex with 20 bp DNA and OSU-276
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9N26
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.75 298 1 ml well solution consisted of 12 % PEG 5000 MME, 0.08 M Bis-Tris pH 5.75, and the hanging drop consisted of 2 ul of well solution mixed with 1 ul of 9.4 mg/ml complex in SEC buffer. Using nylon mounting loops, crystals were fished from the drop, submerged for 30 seconds in a cryo solution containing 15% PEG-5000 MME, 0.08M Bis-Tris pH 6 and 25 % glycerol, then plunged in liquid nitrogen.
Crystal Properties Matthews coefficient Solvent content 2.96 58.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.721 α = 90 b = 92.721 β = 90 c = 402.579 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 S 6M 2025-07-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID 0.97930 APS 31-ID
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 1.836 80.3 88.4 0.15 0.051 0.996 8.3 7.8 117884
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 1.836 2.095 57.7 0.709 0.447 0.265 1.8 3.3
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.836 80.299 117883 6177 69.537 0.172 0.1686 0.1924 0.2381 0.2687 RANDOM 32.078
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] -0.765 -0.765 1.53
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.228 r_dihedral_angle_6_deg 14.675 r_dihedral_angle_2_deg 8.042 r_lrange_it 7.96 r_lrange_other 7.944 r_dihedral_angle_1_deg 7.812 r_scangle_it 5.979 r_scangle_other 5.947 r_mcangle_it 4.858 r_mcangle_other 4.858
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.228 r_dihedral_angle_6_deg 14.675 r_dihedral_angle_2_deg 8.042 r_lrange_it 7.96 r_lrange_other 7.944 r_dihedral_angle_1_deg 7.812 r_scangle_it 5.979 r_scangle_other 5.947 r_mcangle_it 4.858 r_mcangle_other 4.858 r_scbond_it 4.055 r_scbond_other 4.023 r_mcbond_it 3.525 r_mcbond_other 3.521 r_angle_refined_deg 2.116 r_angle_other_deg 0.673 r_dihedral_angle_other_2_deg 0.531 r_symmetry_xyhbond_nbd_refined 0.329 r_symmetry_nbd_refined 0.307 r_xyhbond_nbd_refined 0.261 r_nbd_refined 0.212 r_symmetry_nbd_other 0.197 r_nbtor_refined 0.186 r_nbd_other 0.165 r_chiral_restr 0.091 r_symmetry_nbtor_other 0.086 r_symmetry_xyhbond_nbd_other 0.086 r_bond_refined_d 0.009 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10626 Nucleic Acid Atoms 800 Solvent Atoms 928 Heterogen Atoms 69
Software Software Software Name Purpose REFMAC refinement XDS data reduction STARANISO data scaling PHASER phasing