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3.4A 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 293 10% perg 5k mme, 150mM Bis Tris pH6.2 - see paper for details.
Crystal Properties Matthews coefficient Solvent content 3.2 61.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 187.64 α = 90 b = 410.12 β = 120.22 c = 93.94 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 ADSC QUANTUM 315 2012-04-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I23 0.9795 Diamond I23
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 3.4 162.15 81.1 0.121 0.144 0.077 10.6 3.1 135780
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 3.4 3.58 83.9 0.369 0.44 0.237 3.1
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 MOLECULAR REPLACEMENT THROUGHOUT 2XCS 3.4 162.15 128993 6786 80.35 0.17787 0.17627 0.1788 0.20834 0.2078 RANDOM 53.745
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] 7.76 -1.93 15.83 -23.59
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.382 r_dihedral_angle_4_deg 18.574 r_long_range_B_refined 15.951 r_long_range_B_other 15.951 r_dihedral_angle_3_deg 15.82 r_mcangle_it 8.43 r_mcangle_other 8.43 r_scangle_other 8.069 r_dihedral_angle_1_deg 6.147 r_mcbond_it 5.195
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.382 r_dihedral_angle_4_deg 18.574 r_long_range_B_refined 15.951 r_long_range_B_other 15.951 r_dihedral_angle_3_deg 15.82 r_mcangle_it 8.43 r_mcangle_other 8.43 r_scangle_other 8.069 r_dihedral_angle_1_deg 6.147 r_mcbond_it 5.195 r_mcbond_other 5.195 r_scbond_it 4.944 r_scbond_other 4.944 r_angle_refined_deg 1.479 r_angle_other_deg 1.237 r_chiral_restr 0.058 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_bond_other_d 0.003 r_gen_planes_other 0.002 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 61755 Nucleic Acid Atoms 4642 Solvent Atoms Heterogen Atoms 312
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHENIX phasing