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Human dUTPase in complex with alpha,beta-imido-dUTP and Mg2+: visualization of the full-length C-termini in all monomers and suggestion for an additional metal ion binding site
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, HANGING DROP 7.5 293 0.1 M HEPES buffer, containing 20% PEG 3350 and 200 mM sodium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.89 34.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.446 α = 90 b = 87.16 β = 90.09 c = 70.608 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 MAR CCD 165 mm BENT, VERTICALLY FOCUSING MIRROR 2004-11-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X13 0.8031 EMBL/DESY, HAMBURG X13
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 1.8 20 95.8 0.071 10.15 2.17 70417 70417 -3 26.26
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 1.8 1.9 97.4 0.475 2.24 2.13 10689
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 1.8 20 66842 66842 3574 95.84 0.15972 0.1576 0.1615 0.19898 0.2031 RANDOM 23.11
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] -0.84 -0.07 0.24 0.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.116 r_dihedral_angle_4_deg 17.146 r_dihedral_angle_3_deg 13.382 r_dihedral_angle_1_deg 6.439 r_scangle_it 5.14 r_scbond_it 3.446 r_mcangle_it 1.52 r_angle_refined_deg 1.289 r_mcbond_it 0.875 r_nbtor_refined 0.314
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.116 r_dihedral_angle_4_deg 17.146 r_dihedral_angle_3_deg 13.382 r_dihedral_angle_1_deg 6.439 r_scangle_it 5.14 r_scbond_it 3.446 r_mcangle_it 1.52 r_angle_refined_deg 1.289 r_mcbond_it 0.875 r_nbtor_refined 0.314 r_nbd_refined 0.195 r_symmetry_vdw_refined 0.191 r_symmetry_hbond_refined 0.174 r_xyhbond_nbd_refined 0.156 r_chiral_restr 0.079 r_metal_ion_refined 0.016 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 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_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 6346 Nucleic Acid Atoms Solvent Atoms 731 Heterogen Atoms 176
Software Software Software Name Purpose MOLREP phasing REFMAC refinement XDS data reduction XSCALE data scaling