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Discovery of Novel Uracil Derivatives as Potent Human dUTPase Inhibitors
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 15%~20% PEG 4000, 0.05M Tris buffer, 0.05M magnesium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.87 57.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.89 α = 90 b = 83.263 β = 90 c = 89.662 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 98 IMAGE PLATE RIGAKU RAXIS V 2006-07-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL32B2 1 SPring-8 BL32B2
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 1.7 100 97.5 0.048 5.19 68051 66325
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 1.7 1.76 99.5 0.21 2.6 4.81
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 (All) 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 1.7 61.01 64614 62973 3352 97.46 0.215 0.215 0.21365 0.2049 0.24038 0.2328 RANDOM 23.135
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] -0.02 -0.11 0.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.104 r_dihedral_angle_4_deg 21.461 r_dihedral_angle_3_deg 12.774 r_dihedral_angle_1_deg 7.189 r_scangle_it 5.672 r_scbond_it 3.576 r_mcangle_it 2.461 r_angle_refined_deg 2.256 r_mcbond_it 1.521 r_chiral_restr 0.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.104 r_dihedral_angle_4_deg 21.461 r_dihedral_angle_3_deg 12.774 r_dihedral_angle_1_deg 7.189 r_scangle_it 5.672 r_scbond_it 3.576 r_mcangle_it 2.461 r_angle_refined_deg 2.256 r_mcbond_it 1.521 r_chiral_restr 0.19 r_bond_refined_d 0.029 r_gen_planes_refined 0.014 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2922 Nucleic Acid Atoms Solvent Atoms 387 Heterogen Atoms 101
Software Software Software Name Purpose AMoRE phasing REFMAC refinement CrystalClear data reduction CrystalClear data scaling