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Human dUTP Pyrophosphatase complex with dUDP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DUP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 295 1.1M sodium citrate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.21 44.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.197 α = 90 b = 110.766 β = 90 c = 53.243 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 295 IMAGE PLATE MARRESEARCH mirrors 1996-03-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 25 94 0.077 0.077 10.8 3.62 28406 28406 2 2 15
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.07 82 0.323 0.323 4.4 4 2412
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 1DUP 2 25 26846 26946 1435 94.78 0.17877 0.17877 0.17692 0.1788 0.21426 0.2164 RANDOM 13.189
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] -0.41 0.85 -0.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.821 r_scangle_it 2.384 r_scbond_it 1.41 r_angle_refined_deg 1.094 r_mcangle_it 0.811 r_mcbond_it 0.402 r_nbd_refined 0.166 r_symmetry_hbond_refined 0.149 r_symmetry_vdw_refined 0.133 r_xyhbond_nbd_refined 0.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.821 r_scangle_it 2.384 r_scbond_it 1.41 r_angle_refined_deg 1.094 r_mcangle_it 0.811 r_mcbond_it 0.402 r_nbd_refined 0.166 r_symmetry_hbond_refined 0.149 r_symmetry_vdw_refined 0.133 r_xyhbond_nbd_refined 0.12 r_chiral_restr 0.074 r_bond_refined_d 0.008 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3150 Nucleic Acid Atoms Solvent Atoms 238 Heterogen Atoms 73
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing