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Crystal structure of E. coli Gyrase B co-complexed with PROP-2-YN-1-YL {[5-(4-PIPERIDIN-1-YL-2-PYRIDIN-3-YL-1,3-THIAZOL-5-YL)-1H-PYRAZOL-3-YL]METHYL}CARBAMATE inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1S14
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 298 hanging drop, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.05 59.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.4 α = 90 b = 95.4 β = 90 c = 51.25 γ = 120
Symmetry Space Group P 31 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 120 IMAGE PLATE RIGAKU RAXIS IV mirrors 2006-10-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.2 20 99.3 0.07 13863 13724 2 2 23.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.3 99
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1S14 2.2 19.81 2 13834 13664 685 98.2 0.208 0.206 0.2067 0.234 0.2359 RANDOM 37.3
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] 7.07 6.82 7.07 -14.15
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 21.8 c_scangle_it 2.96 c_mcangle_it 2 c_scbond_it 2 c_mcbond_it 1.27 c_angle_deg 0.9 c_improper_angle_d 0.64 c_bond_d 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1550 Nucleic Acid Atoms Solvent Atoms 99 Heterogen Atoms 30
Software Software Software Name Purpose CrystalClear data collection AMoRE phasing CNX refinement DENZO data reduction SCALEPACK data scaling