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Crystal structure of 24 kDa domain of E. coli DNA gyrase B in complex with small molecule inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1KZN PDB entry 1KZN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.4 293 0.1M MES, 22% PEG 3350, 0.2M NaNO3, pH 6.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.21 44.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.236 α = 90 b = 51.122 β = 95.68 c = 79.13 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD RAYONIX MX-225 Mirrors 2011-12-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.91841 BESSY 14.1
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 1.5 78.74 99.2 0.051 13.8 7.3 68264 67478 1 1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.53 99.6 0.476 7.3 3350
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 1KZN 1.5 20 98264 67460 3420 98.87 0.1932 0.1915 0.2255 0.2294 RANDOM 26.9519
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] -0.66 -0.43 0.46 0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.108 r_dihedral_angle_4_deg 17.271 r_dihedral_angle_3_deg 13.738 r_dihedral_angle_1_deg 6.829 r_scangle_it 6.372 r_scbond_it 3.979 r_mcangle_it 2.829 r_mcbond_it 1.747 r_angle_refined_deg 1.528 r_chiral_restr 0.153
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.108 r_dihedral_angle_4_deg 17.271 r_dihedral_angle_3_deg 13.738 r_dihedral_angle_1_deg 6.829 r_scangle_it 6.372 r_scbond_it 3.979 r_mcangle_it 2.829 r_mcbond_it 1.747 r_angle_refined_deg 1.528 r_chiral_restr 0.153 r_bond_refined_d 0.018 r_gen_planes_refined 0.014
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3008 Nucleic Acid Atoms Solvent Atoms 477 Heterogen Atoms 52
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction MxCuBE data collection PHASER phasing