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Crystal structure of a cis-epoxysuccinate hydrolase producing D(-)-tartaric acids
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2Y7D
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 291 0.1 M sodium chloride, 0.1 M HEPES pH7.0, 1.6 M ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 2.51 55.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.49 α = 90 b = 94.25 β = 95.898 c = 94.36 γ = 90
Symmetry Space Group P 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315r 2013-10-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U1 0.97915 SSRF BL17U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.5 40.35 99.7 0.115 6.7 3.7 216906 15.35
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.55 98.4 0.664 1.8 3.6
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 2Y7D 1.5 40.35 1.35 216879 2000 99.67 0.1491 0.1489 0.1498 0.1702 0.1705 22.65
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 9.9003 f_angle_d 1.0721 f_chiral_restr 0.0706 f_bond_d 0.0105 f_plane_restr 0.0083
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8806 Nucleic Acid Atoms Solvent Atoms 1524 Heterogen Atoms 4
Software Software Software Name Purpose phenix.refine refinement PHENIX refinement XDS data reduction XDS data scaling PHASER phasing ARP/wARP model building