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Crystal Structure of the Cofactor-binding Domain of the Human Phase II Drug Metabolism Enzyme UGT2B15
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 18% PEG 3350, 0.2M Na-Tartrate, 0.2M KCl, 2% glycerol
Crystal Properties Matthews coefficient Solvent content 2.13 42.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.067 α = 90 b = 141.824 β = 115.58 c = 56.884 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 3 1 x-ray 100 CCD ADSC QUANTUM 315r 2018-05-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 3 SYNCHROTRON SSRF BEAMLINE BL17U 0.979 SSRF BL17U
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 3 1.775 70.91 99.25 0.104 0.04 0.991 22.64 6.6 64886
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 3 1.78 1.84 0.521 0.206 0.902 2.737
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 SAD THROUGHOUT 1.78 70.91 64886 3429 99.25 0.14749 0.1457 0.1595 0.18025 0.1922 RANDOM 26.014
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] 3.17 -0.54 -1.02 -1.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.495 r_dihedral_angle_4_deg 13.398 r_dihedral_angle_3_deg 12.994 r_long_range_B_refined 7.333 r_long_range_B_other 7.333 r_dihedral_angle_1_deg 6.635 r_scangle_other 5.602 r_scbond_it 3.817 r_scbond_other 3.816 r_mcangle_it 3.251
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.495 r_dihedral_angle_4_deg 13.398 r_dihedral_angle_3_deg 12.994 r_long_range_B_refined 7.333 r_long_range_B_other 7.333 r_dihedral_angle_1_deg 6.635 r_scangle_other 5.602 r_scbond_it 3.817 r_scbond_other 3.816 r_mcangle_it 3.251 r_mcangle_other 3.25 r_mcbond_it 2.358 r_mcbond_other 2.354 r_angle_refined_deg 1.964 r_angle_other_deg 1.093 r_chiral_restr 0.127 r_bond_refined_d 0.022 r_gen_planes_refined 0.011 r_bond_other_d 0.003 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5180 Nucleic Acid Atoms Solvent Atoms 655 Heterogen Atoms 64
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALA data scaling SHELXCD phasing