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E. eligens beta-glucuronidase bound to UNC10201652-glucuronide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6BJQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.07 M BICINE, pH 9.0, 1.4 % (w/v) 1,4-Dioxane, 7 % (w/v) PEG 20,000, and 30 % (v/v) glycerol
Crystal Properties Matthews coefficient Solvent content 4.49 72.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 180.304 α = 90 b = 180.304 β = 90 c = 133.566 γ = 120
Symmetry Space Group P 64 2 2
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 PILATUS3 6M 2021-08-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 1.0 APS 23-ID-D
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 2.94 48.5 93.48 0.1547 0.1659 0.05804 0.996 10.83 7.2 25959 86.82
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 2.94 3.05 90.81 1.874 2.014 0.7169 0.361 1.16 7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 FREE R-VALUE 2.94 48.5 1.34 25955 2000 93.52 0.2507 0.2485 0.2489 0.2771 0.2756 79.31
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 18.4776 f_angle_d 0.8433 f_chiral_restr 0.0512 f_plane_restr 0.0049 f_bond_d 0.0044
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4608 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 41
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHASER phasing