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Crystal structure of dUTPase complexed with substrate analogue methylene-dUTP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1EUW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.8 293 20% PEG 3350, 0.2M SODIUM ACETATE, 0.1M TRIS, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.57 52.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.65 α = 90 b = 75.65 β = 90 c = 101.558 γ = 120
Symmetry Space Group P 63 2 2
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 mirror M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE BW7B 0.8500 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 1.7 20 99.1 0.048 14.5 3.16 19276 19276 -3 28.27
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 1.7 1.8 99.4 0.457 2.4 3.19 3034
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1EUW 1.7 20 18283 18283 987 99.13 0.16956 0.16956 0.16823 0.19559 0.2017 RANDOM 21.045
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] -0.01 -0.01 -0.01 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.746 r_dihedral_angle_4_deg 20.198 r_dihedral_angle_3_deg 12.259 r_scangle_it 6.903 r_dihedral_angle_1_deg 5.482 r_scbond_it 5.33 r_mcangle_it 2.926 r_mcbond_it 1.702 r_angle_refined_deg 1.677 r_angle_other_deg 0.861
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.746 r_dihedral_angle_4_deg 20.198 r_dihedral_angle_3_deg 12.259 r_scangle_it 6.903 r_dihedral_angle_1_deg 5.482 r_scbond_it 5.33 r_mcangle_it 2.926 r_mcbond_it 1.702 r_angle_refined_deg 1.677 r_angle_other_deg 0.861 r_symmetry_vdw_other 0.213 r_nbd_refined 0.19 r_nbd_other 0.182 r_xyhbond_nbd_refined 0.173 r_symmetry_hbond_refined 0.17 r_nbtor_refined 0.158 r_symmetry_vdw_refined 0.135 r_mcbond_other 0.116 r_chiral_restr 0.112 r_nbtor_other 0.081 r_bond_refined_d 0.019 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1012 Nucleic Acid Atoms Solvent Atoms 136 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing