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Bacteriodes uniformis beta-glucuronidase 1 bound to D-glucaro-1,5-lactone
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6D1N
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293.15 16% PEG 1000, Tris pH 8.5, 2mM Saccharolactone
Crystal Properties Matthews coefficient Solvent content 2.72 54.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 126.066 α = 90 b = 130.156 β = 100.24 c = 94.49 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 PIXEL DECTRIS PILATUS3 6M 2017-04-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 1.03322 APS 23-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.9 29.934 97.7 16.6 6.9 114979
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.93
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 FREE R-VALUE 6D1N 1.9 29.934 1.34 114965 2003 97.65 0.1404 0.1399 0.1402 0.1686 0.169
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 15.781 f_angle_d 0.855 f_chiral_restr 0.057 f_bond_d 0.007 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9520 Nucleic Acid Atoms Solvent Atoms 1501 Heterogen Atoms 76
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHENIX phasing