☰ Navigation Tabs
Crystal Structure of Human Uridine Diphosphate Glucose Pyrophosphatase (NUDT14)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1G0S PDB entries 1G0S, 1VIQ, 1VIU and 2DSB experimental model PDB 1VIQ PDB entries 1G0S, 1VIQ, 1VIU and 2DSB experimental model PDB 1VIU PDB entries 1G0S, 1VIQ, 1VIU and 2DSB experimental model PDB 2DSB PDB entries 1G0S, 1VIQ, 1VIU and 2DSB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 20 % w/v PEG3350, 0.2 M AMMONIUM FORMATE, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.5 50.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.04 α = 90 b = 106.24 β = 90 c = 106.35 γ = 90
Symmetry Space Group P 2 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 RAYONIX MX-225 MIRRORS 2009-06-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.2 0.91841 BESSY 14.2
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 2.7 53.17 99.7 0.063 0.063 8.5 4.8 26804 26724 -3 83.8
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) 2.7 2.85 99.5 0.708 0.708 2.1 4.8 3827
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 entries 1G0S, 1VIQ, 1VIU and 2DSB 2.7 53.17 25328 1376 99.53 0.23054 0.22844 0.2244 0.27137 0.2634 RANDOM 68.955
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] 4.87 -2.13 -2.74
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.676 r_dihedral_angle_3_deg 15.718 r_dihedral_angle_4_deg 12.61 r_dihedral_angle_1_deg 6.158 r_scangle_it 1.438 r_angle_refined_deg 1.068 r_scbond_it 0.84 r_angle_other_deg 0.767 r_mcangle_it 0.628 r_mcbond_it 0.322
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.676 r_dihedral_angle_3_deg 15.718 r_dihedral_angle_4_deg 12.61 r_dihedral_angle_1_deg 6.158 r_scangle_it 1.438 r_angle_refined_deg 1.068 r_scbond_it 0.84 r_angle_other_deg 0.767 r_mcangle_it 0.628 r_mcbond_it 0.322 r_chiral_restr 0.061 r_mcbond_other 0.048 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4399 Nucleic Acid Atoms Solvent Atoms 5 Heterogen Atoms
Software Software Software Name Purpose PHASER phasing REFMAC refinement XDS data reduction SCALA data scaling