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The glucuronoyl esterase OtCE15A H408A variant from Opitutus terrae in complex with, and covalently linked to, 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 298 Protein mixed 50/50 with reservoir solution of 0.2 M Ammonium formate None 20 % w/v PEG 3350
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.104 α = 76.095 b = 44.15 β = 66.231 c = 50.179 γ = 70.854
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 6M 2019-05-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, DESY BEAMLINE P11 1.0332 PETRA III, DESY P11
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 1.749 45.56 95.48 0.09829 0.1169 0.06242 0.994 6.62 3.4 30662 22.59
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 1.749 1.812 88.67 0.8285 0.9829 0.5228 0.736 1.53 3.4
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 1.75 45.56 1.93 30624 2286 95.41 0.2189 0.2136 0.2144 0.2836 0.2834 38.37
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 21.5356 f_angle_d 1.1812 f_chiral_restr 0.0603 f_bond_d 0.0115 f_plane_restr 0.0088
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3075 Nucleic Acid Atoms Solvent Atoms 109 Heterogen Atoms 15
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHENIX phasing