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Human dUTPase in complex with novel uracil derivative
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 15~20% PEG 4000, 50mM Tris, 0.1M magnesium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.88 57.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.404 α = 90 b = 83.147 β = 90 c = 89.586 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 1.8 60 99.6 0.04 6.97 57688 57479
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 1.8 1.86 99.1 0.119 11.8 6.37
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.8 58.53 54568 2911 99.64 0.17194 0.17052 0.1707 0.19794 0.1958 RANDOM 17.222
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.413 r_dihedral_angle_4_deg 21.599 r_dihedral_angle_3_deg 12.939 r_dihedral_angle_1_deg 6.511 r_scangle_it 6.164 r_scbond_it 4.055 r_mcangle_it 2.466 r_angle_refined_deg 2.443 r_mcbond_it 1.525 r_chiral_restr 0.481
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.413 r_dihedral_angle_4_deg 21.599 r_dihedral_angle_3_deg 12.939 r_dihedral_angle_1_deg 6.511 r_scangle_it 6.164 r_scbond_it 4.055 r_mcangle_it 2.466 r_angle_refined_deg 2.443 r_mcbond_it 1.525 r_chiral_restr 0.481 r_bond_refined_d 0.032 r_gen_planes_refined 0.015 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 421 Heterogen Atoms 84
Software Software Software Name Purpose AMoRE phasing REFMAC refinement CrystalClear data reduction CrystalClear data scaling