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UDP-glucuronosyltransferase2B17 C-terminal domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6IPB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 20% PEG 6000, 0.2M Na-Tartrate, 0.2M KCl, 2% glycerol
Crystal Properties Matthews coefficient Solvent content 1.89 34.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.15 α = 99.245 b = 57.308 β = 94.715 c = 74.074 γ = 90.118
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 200K 2021-06-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.54184
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.5 19.11 97.45 0.0978 0.985 8.05 2.7 20837
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.589 0.893
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 6IPB 2.5 19.11 20837 1012 97.469 0.271 0.2677 0.2699 0.3308 0.334 18.094
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] 0.008 0.001 0.025 0.002 -0.027 -0.006
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.607 r_dihedral_angle_3_deg 17.184 r_dihedral_angle_4_deg 15.802 r_dihedral_angle_1_deg 7.858 r_lrange_other 4.689 r_lrange_it 4.688 r_mcangle_it 2.153 r_mcangle_other 2.153 r_scangle_it 1.917 r_scangle_other 1.917
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.607 r_dihedral_angle_3_deg 17.184 r_dihedral_angle_4_deg 15.802 r_dihedral_angle_1_deg 7.858 r_lrange_other 4.689 r_lrange_it 4.688 r_mcangle_it 2.153 r_mcangle_other 2.153 r_scangle_it 1.917 r_scangle_other 1.917 r_angle_refined_deg 1.459 r_mcbond_it 1.225 r_mcbond_other 1.224 r_angle_other_deg 1.138 r_scbond_it 1.108 r_scbond_other 1.108 r_symmetry_xyhbond_nbd_refined 0.414 r_nbd_other 0.336 r_symmetry_nbd_refined 0.304 r_nbd_refined 0.211 r_symmetry_nbd_other 0.198 r_xyhbond_nbd_refined 0.182 r_nbtor_refined 0.156 r_symmetry_xyhbond_nbd_other 0.143 r_symmetry_nbtor_other 0.085 r_chiral_restr 0.051 r_bond_refined_d 0.006 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 5052 Nucleic Acid Atoms Solvent Atoms 46 Heterogen Atoms 40
Software Software Software Name Purpose REFMAC refinement CrysalisPro data reduction SCALA data scaling MOLREP phasing