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DNA gyrase complexed with uncleaved DNA and Compound 7 to 2.6A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2XCS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.2 298 motherliquor: 80mM Bis-Tris, pH=6.2, 15.33% PEG 5000MME
protein: 50mM HEPES, pH=7.5
1.2uL motherliquor : 0.8uL protein
streaked with existing seed stock
Crystal Properties Matthews coefficient Solvent content 3.01 59.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.017 α = 90 b = 93.017 β = 90 c = 406.663 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 77 PIXEL DECTRIS PILATUS3 6M 2020-11-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 1.54 APS 19-ID
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 2.601 23.7427486328 98.87 0.22 0.239 0.093 0.997 9.2 6.1 60022 61.3801855894
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.601 2.694 90.81 0.66 0.389
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 NONE 2XCS 2.60137142659 23.7427486328 1.33788961277 60022 3878 97.216123286 0.19732038353 0.195513593603 0.1948 0.251722343658 0.2519 77.4825563237
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 17.1374182196 f_angle_d 0.507407405598 f_chiral_restr 0.0401003713926 f_bond_d 0.00329705531821 f_plane_restr 0.00300558890709
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10627 Nucleic Acid Atoms 800 Solvent Atoms 145 Heterogen Atoms 44
Software Software Software Name Purpose SBC-Collect data collection PHENIX refinement HKL-2000 data reduction HKL-2000 data scaling PHENIX phasing