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2.7A structure of benzoisoxazole 3 with S.aureus DNA gyrase and DNA.
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 MICROBATCH 6.2 293 11% PEG 5000MME, 150mM BisTris pH6.2
Crystal Properties Matthews coefficient Solvent content 3.04 59.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.19 α = 90 b = 93.19 β = 90 c = 408.99 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 PILATUS 6M 2012-03-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9763 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.65 58.43 98.4 0.063 0.076 0.042 12.4 3 57152
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.65 2.79 99.2 0.529 0.645 0.36 2.5 3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 FOURIER SYNTHESIS THROUGHOUT 2XCS 2.65 57.52 54124 2904 98.38 0.16429 0.16211 0.1636 0.20615 0.208 RANDOM 60.688
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] -0.46 -0.23 -0.46 1.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.018 r_dihedral_angle_4_deg 20.466 r_dihedral_angle_3_deg 16.975 r_long_range_B_refined 10.751 r_dihedral_angle_1_deg 6.501 r_mcangle_it 4.218 r_scbond_it 3.758 r_mcbond_it 2.64 r_angle_refined_deg 2.128 r_chiral_restr 0.141
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.018 r_dihedral_angle_4_deg 20.466 r_dihedral_angle_3_deg 16.975 r_long_range_B_refined 10.751 r_dihedral_angle_1_deg 6.501 r_mcangle_it 4.218 r_scbond_it 3.758 r_mcbond_it 2.64 r_angle_refined_deg 2.128 r_chiral_restr 0.141 r_bond_refined_d 0.016 r_gen_planes_refined 0.012 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10582 Nucleic Acid Atoms 807 Solvent Atoms 331 Heterogen Atoms 89
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALA data scaling REFMAC phasing