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Crystal Structure of a P. Aeruginosa Gyrase Chimera In Complex with 20mer DNA and Ciprofloxacin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other coordinates from apo structure being co-deposited
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 294 0.1M sodium citrate pH 6.0
14% PEG 4000
200mM Ammonium Sulfate
1mM MnCl2
1mM ciprofloxacin
Crystal Properties Matthews coefficient Solvent content 3.39 63.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 179.033 α = 90 b = 179.033 β = 90 c = 163.298 γ = 120
Symmetry Space Group P 63 2 2
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 EIGER X 16M 2021-10-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.000 APS 22-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 2.85 50 99.2 0.168 0.174 0.043 0.992 3.7 15.5 36343 51.72
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 2.85 2.9 1.252 1.296 0.327 0.815 1.29
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 2.85 43.67 1.35 36096 1800 98.57 0.2065 0.205 0.2049 0.2344 0.2337 58.3
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 17.3859 f_angle_d 0.9544 f_chiral_restr 0.0524 f_plane_restr 0.0088 f_bond_d 0.0078
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5674 Nucleic Acid Atoms 407 Solvent Atoms 16 Heterogen Atoms 85
Software Software Software Name Purpose PHENIX refinement PHENIX refinement HKL-3000 data reduction HKL-3000 data scaling PHASER phasing