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HUMAN DUTP PYROPHOSPHATASE
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 2.19 43.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.991 α = 90 b = 110.666 β = 90 c = 52.954 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 1995-04-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.5418
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 30 97.5 0.091 0.091 8.3 3.5 29007 29007 2 2 20
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 98.9 0.453 0.453 3.2 3 2900
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 27503 27503 1467 97.5 0.18965 0.18965 0.1878 0.1886 0.22582 0.2242 RANDOM 16.244
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 -0.67 1.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.821 r_scangle_it 2.061 r_scbond_it 1.21 r_angle_refined_deg 0.987 r_mcangle_it 0.746 r_mcbond_it 0.374 r_nbd_refined 0.168 r_symmetry_vdw_refined 0.149 r_symmetry_hbond_refined 0.128 r_xyhbond_nbd_refined 0.126
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.821 r_scangle_it 2.061 r_scbond_it 1.21 r_angle_refined_deg 0.987 r_mcangle_it 0.746 r_mcbond_it 0.374 r_nbd_refined 0.168 r_symmetry_vdw_refined 0.149 r_symmetry_hbond_refined 0.128 r_xyhbond_nbd_refined 0.126 r_chiral_restr 0.069 r_bond_refined_d 0.007 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3057 Nucleic Acid Atoms Solvent Atoms 304 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing