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Native Glucuronoyl Esterase from Opitutus terrae
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6GRW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 293.15 Reservoir composition: 0.3 M Sodium phosphate dibasic dihydrate, 0.3 M Ammonium sulfate and 0.3 M Sodium nitrate, 0.05 M Tris and 0,05 M BICINE, 12.5 % v/v MPD, 12.5 % w/v PEG1000 and 12.5 % w/v PEG3350
Drop size and composition: sitting drops of 0.3 ul were mixed in a protein:reservoir volume ratio of 3:1 using 45 mg/ml of OtCE15A in 20 mM TRIS pH 8.0
Crystal Properties Matthews coefficient Solvent content 1.9 35.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.361 α = 75.863 b = 44.263 β = 66.326 c = 50.027 γ = 70.876
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 2017-04-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.9 ESRF ID30B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 1.34 45.43 88.9 0.092 0.101 0.995 6.35 2.95 63925 14.79
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.34 1.37 88.6 1.073 1.159 0.534 0.97 2.93
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 6GRW 1.34 45.43 1.94 63886 2645 89.06 0.1745 0.173 0.1734 0.2073 0.2066 22.56
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 18.3092 f_angle_d 1.0739 f_chiral_restr 0.0749 f_plane_restr 0.0086 f_bond_d 0.0081
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3074 Nucleic Acid Atoms Solvent Atoms 366 Heterogen Atoms 52
Software Software Software Name Purpose PHENIX refinement Coot model building XDS data reduction PHENIX phasing XDS data scaling