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Crystal Structure of the UDPGA Binding Domain of the Human Phase II Metabolizing Enzyme UDP-Glucuronosyltransferase 2B10
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2O6L
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 5 292 0.1 M sodium citrate pH 5.0, 2.5 M AMS, 10% glycerol
Crystal Properties Matthews coefficient Solvent content 2.3 46.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.907 α = 90 b = 58.387 β = 98.14 c = 68.867 γ = 90
Symmetry Space Group C 1 2 1
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-300 2022-01-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17B1 0.97918 SSRF BL17B1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 1.527 48.13 94.8 0.105 0.115 0.046 0.994 14.2 4.9 48413 23.45
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.53 1.61 90.4 0.664 0.775 0.389 0.695 3.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2O6L 1.527 34.087 1.34 48114 2406 93.91 0.217 0.2155 0.216 0.2446 0.2437 30.7855
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 14.975 f_angle_d 0.864 f_chiral_restr 0.054 f_bond_d 0.009 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2608 Nucleic Acid Atoms Solvent Atoms 165 Heterogen Atoms 5
Software Software Software Name Purpose PHENIX refinement Aimless data scaling PDB_EXTRACT data extraction autoPROC data reduction PHENIX phasing