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Structure of oxaloacetate acetylhydrolase in complex with the product oxalate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3LYE PDB ENTRY 3LYE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 LIGAND-FREE PROTEIN CRYSTAL GROWN IN SOLUTION CONTAINING 30% PEG 400, 0.1 M HEPES pH7.5, 0.2 M CaCl2, THEN SOAKED IN MOTHER LIQUOR CONTAINING 0.2M MNCL2 AND 50 mM OXALOACETATE (the substrate) FOR 15 min, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 1.85 33.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.131 α = 90 b = 82.131 β = 90 c = 72.717 γ = 90
Symmetry Space Group P 42 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE MAR scanner 345 mm plate M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
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 1.65 20 99.8 0.076 22.3 11 30531 30472 14.5
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) 1.65 1.69 99.8 0.51 3 7.1
Refinement Statistics Diffraction ID Structure Solution 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 PDB ENTRY 3LYE 1.65 19.92 1.48 30472 1552 99.9 0.174 0.172 0.1739 0.201 0.2068 21.98
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] -0.327 -0.327 0.465
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 16 f_angle_d 0.862 f_chiral_restr 0.062 f_bond_d 0.005 f_plane_restr 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2179 Nucleic Acid Atoms Solvent Atoms 306 Heterogen Atoms 8
Software Software Software Name Purpose PHASER phasing PHENIX refinement XDS data reduction XSCALE data scaling