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P. putida mandelate racemase forms an oxobenzoxaborole adduct with 2-formylphenylboronic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3UXK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 298 Reservoir solution: PEG 3350 (3% w/v), Bis-Tris Propane (50 mM)
Protein solution:P. putida mandelate racemase (6 mg/mL), 2-formylphenylboronic acid (1.0 mM), MgCl2 (3.3 mM), and Na+-HEPES buffer (50 mM, pH 7.5)
The protein solution and reservoir solution were mixed in a 1:1 ratio to a final volume of 10 microliters
Crystal Properties Matthews coefficient Solvent content 2.97 58.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 225.483 α = 90 b = 149.43 β = 129.34 c = 149.523 γ = 90
Symmetry Space Group C 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 DECTRIS EIGER X 9M 2019-08-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 1.12709 APS 21-ID-D
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 1.91 113.47 99.3 0.187 0.203 0.078 0.99 7.9 6.8 291736 20.15
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 1.914 1.947 98.4 1.012 1.099 0.42 0.721 2.1 6.7
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 THROUGHOUT 3UXK 1.914 40.606 1.35 291503 14797 99.28 0.1886 0.1872 0.1874 0.2147 0.2147 21.3997
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]
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 21487 Nucleic Acid Atoms Solvent Atoms 2153 Heterogen Atoms 192
Software Software Software Name Purpose Aimless data scaling PHASER phasing PHENIX refinement PDB_EXTRACT data extraction XDS data reduction