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Crystal structure of Variovorax paradoxus indole monooxygenase (VpIndA1) in complex with indole
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7Z4X
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 A solution of 13.6 mg/mL protein was supplemented with 6.2 mM FAD, 18.4 mM indole and 6.2 % (v/v) DMSO and mixed in a 1:1 ratio with 100 mM Tris/HCl (pH 8.5) and 2 M ammonium sulfate. Crystals were cryo-protected by swiping them through 50 mM Tris/HCl (pH 8.5), 2.3 M ammonium sulfate, 12 % (v/v) ethylene glycol, 3 mM FAD and 10 mM indole.
Crystal Properties Matthews coefficient Solvent content 2.98 58.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.938 α = 90 b = 93.938 β = 90 c = 110.867 γ = 120
Symmetry Space Group P 32 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 PIXEL DECTRIS PILATUS 6M 2021-02-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.9184 BESSY 14.1
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 1.74 46.97 99.9 0.093 0.096 0.024 1 18.3 15.5 58636
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 1.74 1.77 98.2 3.31 3.421 0.861 0.408 15.5
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 FOURIER SYNTHESIS THROUGHOUT 7Z4X 1.74 40.68 1.33 58550 2944 99.89 0.1628 0.1615 0.1652 0.1883 0.191 37.7677
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 3154 Nucleic Acid Atoms Solvent Atoms 264 Heterogen Atoms 221
Software Software Software Name Purpose Aimless data scaling PHENIX refinement PDB_EXTRACT data extraction XDS data reduction REFMAC phasing