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Crystal structure of Ideonella sakaiensis MHETase bound to the non-hydrolyzable ligand MHETA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6G21
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.1 M HEPES, pH 7.5, 30% (v/v) 2,4-MPD and 0.12 M ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 3.37 63.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 112.153 α = 90 b = 183.646 β = 90 c = 246.752 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 PILATUS3 2M 2018-06-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.2 0.9184 BESSY 14.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.1 50 98.9 0.195 0.212 0.993 8.85 6.5 293388 32.3
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 2.1 2.22 93.4 1.054 1.18 0.602 1.3 4.9
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 6G21 2.1 49.107 1.35 293303 3081 98.86 0.1733 0.1731 0.1744 0.198 0.1911
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 13.561 f_angle_d 1.04 f_chiral_restr 0.062 f_bond_d 0.01 f_plane_restr 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 24746 Nucleic Acid Atoms Solvent Atoms 2640 Heterogen Atoms 226
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling MoRDa phasing