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Structure of proline utilization A complexed with 2,3-dihydro-1,4-benzodioxine-5-carboxylic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6X9A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 Reservoir contained 0.1 M HEPES, pH 7.5, 0.1 M sodium formate, 0.1 M magnesium chloride, 0.25 M ammonium sulfate, and 18% (w/v) PEG 3350. Enzyme was incubated with 10 mM 2,3-dihydro-1,4-benzodioxine-5-carboxylic acid and 5 mM NAD+. Crystal was soaked in cryobuffer containing 50 mM 2,3-dihydro-1,4-benzodioxine-5-carboxylic acid and 20% PEG 200
Crystal Properties Matthews coefficient Solvent content 2.35 47.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.396 α = 90 b = 101.723 β = 106.23 c = 126.293 γ = 90
Symmetry Space Group P 1 21 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 PIXEL DECTRIS EIGER2 S 9M 2023-10-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.1 1.000034 ALS 8.2.1
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 1.55 48.2 98.3 0.046 0.055 0.029 0.998 14.1 3.4 658070
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 1.55 1.58 99.6 0.716 0.844 0.442 0.65 3.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 FOURIER SYNTHESIS FREE R-VALUE 1.55 46.9 0.05 658070 32861 94.47 0.1685 0.1674 0.1659 0.1896 0.1876
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 16.697 f_angle_d 0.867 f_chiral_restr 0.048 f_plane_restr 0.008 f_bond_d 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 17811 Nucleic Acid Atoms Solvent Atoms 2311 Heterogen Atoms 334
Software Software Software Name Purpose PHENIX refinement Aimless data scaling XDS data reduction PHASER phasing