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Crystal structural analysis of Drosophila melanogaster dUTPase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1Q5U PDB ENTRY 1Q5U
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 297 50 mM sodium succinate buffer, 200 mM sodium chloride, 30-35% methyl-pentane diol, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 297K
Crystal Properties Matthews coefficient Solvent content 2.23 44.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.799 α = 90 b = 42.799 β = 90 c = 169.384 γ = 90
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE MAR scanner 345 mm plate mirrors M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE BW7B 0.8457 EMBL/DESY, HAMBURG BW7B
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 1.78 20 99.1 0.068 14.95 7.45 28229 28229 -3 41.2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.78 1.89 95.6 0.74 2.3 6.84 4348
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 PDB ENTRY 1Q5U 1.88 20 23345 23345 1225 99.77 0.20152 0.20048 0.2056 0.22221 0.2256 RANDOM 41.067
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] 0.62 0.62 -1.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.792 r_dihedral_angle_3_deg 15.143 r_dihedral_angle_4_deg 15.038 r_dihedral_angle_1_deg 7.84 r_scangle_it 7.069 r_scbond_it 4.471 r_mcangle_it 3.096 r_mcbond_it 2.17 r_angle_refined_deg 1.938 r_nbtor_refined 0.318
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.792 r_dihedral_angle_3_deg 15.143 r_dihedral_angle_4_deg 15.038 r_dihedral_angle_1_deg 7.84 r_scangle_it 7.069 r_scbond_it 4.471 r_mcangle_it 3.096 r_mcbond_it 2.17 r_angle_refined_deg 1.938 r_nbtor_refined 0.318 r_symmetry_vdw_refined 0.283 r_nbd_refined 0.244 r_symmetry_hbond_refined 0.238 r_xyhbond_nbd_refined 0.204 r_chiral_restr 0.138 r_bond_refined_d 0.021 r_gen_planes_refined 0.009 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other 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 1770 Nucleic Acid Atoms Solvent Atoms 111 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing