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Human dUTPase in complex with alpha,beta-iminodUTP and magnesium ion
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1Q5U PDB entry 1Q5U truncated at residue 146
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 18-20% PEG 3350, 0.1M Na-Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.68 26.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.409 α = 90 b = 71.773 β = 90 c = 76.475 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 100 CCD MAR CCD 165 mm mirror M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X11 0.8124 EMBL/DESY, HAMBURG X11
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 2.1 20 99.1 0.116 9.21 1.2 21420 21420 -3 28.8
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 2.1 2.2 99 0.33 3.69 1.2 2736
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 (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 PDB entry 1Q5U truncated at residue 146 2.2 20 17739 17739 945 99.11 0.20223 0.20223 0.19968 0.2053 0.25065 0.259 RANDOM 20.252
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] -2.1 -0.92 3.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.176 r_dihedral_angle_4_deg 22.048 r_dihedral_angle_3_deg 17.468 r_dihedral_angle_1_deg 6.536 r_scangle_it 2.256 r_scbond_it 1.571 r_angle_refined_deg 1.415 r_mcangle_it 0.863 r_mcbond_it 0.497 r_nbtor_refined 0.315
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.176 r_dihedral_angle_4_deg 22.048 r_dihedral_angle_3_deg 17.468 r_dihedral_angle_1_deg 6.536 r_scangle_it 2.256 r_scbond_it 1.571 r_angle_refined_deg 1.415 r_mcangle_it 0.863 r_mcbond_it 0.497 r_nbtor_refined 0.315 r_symmetry_vdw_refined 0.283 r_nbd_refined 0.21 r_xyhbond_nbd_refined 0.187 r_symmetry_hbond_refined 0.179 r_metal_ion_refined 0.118 r_chiral_restr 0.086 r_bond_refined_d 0.012 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3022 Nucleic Acid Atoms Solvent Atoms 152 Heterogen Atoms 89
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing