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The glucuronoyl esterase OtCE15A H408A variant from Opitutus terrae
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 Morpheus screen solution C12: 0.09 M NPS (0.3M Sodium nitrate, 0.3 Sodium phosphate dibasic, 0.3M Ammonium sulfate), 0.1 M Buffer System 3 pH 8.5 (Tris; BICINE), 50 % v/v Precipitant Mix 4 (25% v/v MPD; 25% PEG 1000; 25% w/v PEG 3350)
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.197 α = 76.31 b = 44.204 β = 65.696 c = 50.154 γ = 70.744
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 1.738 45.39 94.21 0.04631 0.055 0.0293 0.998 14.6 3.4 30758 21.89
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 1.738 1.8 76.75 0.3377 0.4005 0.2129 0.945 2.85 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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6gs0 1.74 45.39 1.93 30727 2306 94.21 0.1459 0.1423 0.1921 0.196 32.06
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 17.575 f_angle_d 1.0057 f_chiral_restr 0.0573 f_bond_d 0.0089 f_plane_restr 0.0071
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3063 Nucleic Acid Atoms Solvent Atoms 223 Heterogen Atoms 35
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHENIX phasing