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The glucuronoyl esterase OtCE15A S267A variant from Opitutus terrae in complex with benzyl D-glucuronoate and D-glucuronate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6GS0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 298 Enzyme mixed 50/50 with reservoir solution containing JCSG+ screen solution G4: 0.2 M Trimethylamine N-oxide, 0.1 M Tris pH 8.5, and 20 % w/v PEG 2000 MME
Crystal Properties Matthews coefficient Solvent content 2.14 42.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.719 α = 90 b = 87.611 β = 90 c = 173.91 γ = 90
Symmetry Space Group P 21 21 21
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 EIGER X 4M 2018-12-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-3 0.9677 ESRF MASSIF-3
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 1.89 44.45 98.98 0.1589 0.1651 0.04436 0.999 12.25 13.6 63514 33.05
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.89 1.96 92 0.6206 0.403 0.84 13.4
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 6gs0 1.89 44.45 1.33 63362 1988 98.63 0.1638 0.1622 0.1645 0.2155 0.2169 39.74
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 22.8048 f_angle_d 1.121 f_chiral_restr 0.0623 f_bond_d 0.0105 f_plane_restr 0.0079
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6081 Nucleic Acid Atoms Solvent Atoms 412 Heterogen Atoms 344
Software Software Software Name Purpose XDS data reduction XDS data scaling PHENIX phasing PHENIX refinement