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Crystal structure of a topoisomerase ATP inhibitor
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 18-25% Peg4000, 0.2M Ammonium Acetate, 0.1M MIB pH 7, inhibitor soak, temperature 293K, VAPOR DIFFUSION, HANGING DROP
Crystal Properties Matthews coefficient Solvent content 2.18 43.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.875 α = 90 b = 94.333 β = 90 c = 62.27 γ = 90
Symmetry Space Group C 2 2 21
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 monochromator 2007-05-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID 1.000 APS 31-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.955 62.27 99.8 0.084 16.3 7.1 15850 15850
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.95 2.06 100 0.386 0.386 2 7.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) 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 1.95 57.67 15830 15042 788 99.5 0.16816 0.16638 0.1755 0.20197 0.2059 RANDOM 26.36
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 -0.4 -0.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.767 r_dihedral_angle_4_deg 15.412 r_dihedral_angle_3_deg 13.348 r_dihedral_angle_1_deg 5.803 r_scbond_it 3.226 r_mcangle_it 3.028 r_mcbond_other 2.299 r_mcbond_it 2.298 r_angle_refined_deg 1.67 r_angle_other_deg 0.825
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.767 r_dihedral_angle_4_deg 15.412 r_dihedral_angle_3_deg 13.348 r_dihedral_angle_1_deg 5.803 r_scbond_it 3.226 r_mcangle_it 3.028 r_mcbond_other 2.299 r_mcbond_it 2.298 r_angle_refined_deg 1.67 r_angle_other_deg 0.825 r_chiral_restr 0.101 r_bond_refined_d 0.018 r_gen_planes_refined 0.008 r_bond_other_d 0.005 r_gen_planes_other 0.001 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_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined 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 1480 Nucleic Acid Atoms Solvent Atoms 107 Heterogen Atoms 30
Software Software Software Name Purpose SCALA data scaling AMoRE phasing REFMAC refinement PDB_EXTRACT data extraction XSCALE data scaling