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The glucuronoyl esterase OtCE15A S267A variant from Opitutus terrae in complex with D-galacturonate
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 7.5 298 Enzyme mixed 50/50 with reservoir solution containing Morpheus screen solution E8: 0.12 M Ethylene glycols (0.3M Diethylene glycol; 0.3M Triethylene glycol; 0.3M Tetraethylene glycol; 0.3M Pentaethylene glycol), 0.1 M Buffer System 2 pH 7.5 (Sodium HEPES; MOPS), and 50 % v/v Precipitant Mix 4 (25% v/v MPD; 25% PEG 1000; 25% w/v PEG 3350)
Crystal Properties Matthews coefficient Solvent content 1.89 34.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.626 α = 63.653 b = 46.138 β = 86.794 c = 50.195 γ = 71.166
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 2018-09-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, DESY BEAMLINE P11 0.9891 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 2.198 44.74 97.04 0.08127 0.1006 0.05835 0.996 8.66 2.7 16711 30.4
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 2.198 2.277 94.62 0.4798 0.594 0.3448 0.747 2 2
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 2.2 44.74 1.98 16672 1249 97.04 0.1594 0.1543 0.1549 0.221 0.2216 35.1
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 24.1717 f_angle_d 1.2617 f_chiral_restr 0.0628 f_bond_d 0.0116 f_plane_restr 0.0086
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2782 Nucleic Acid Atoms Solvent Atoms 122 Heterogen Atoms 194
Software Software Software Name Purpose XDS data reduction XDS data scaling PHENIX phasing PHENIX refinement