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Crystal structure of the L-arginine hydroxylase VioC MeHis316, bound to Fe(II), L-arginine, and succinate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6ALQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 final concentration of 10 mg ml-1 protein, in 20 mM HEPES buffer pH 7.5 containing 0.4 mM ammonium iron(II) sulphate hexahydrate, 2 mM L-arginine and 2 mM succinate, mixed 1:1 volume with 0.02 M magnesium chloride hexahydrate, 0.1 M HEPES, pH 7.5, containing 22 % (w/v) poly(acrylic acid sodium salt) 5100
Crystal Properties Matthews coefficient Solvent content 1.87 34.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.145 α = 90 b = 67.107 β = 109.221 c = 62.945 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 PIXEL DECTRIS EIGER2 S 16M 2020-10-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.976 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.6 38.48 99.61 0.999 15.47 6.6 41962 17.87
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.64 96.09 0.922 1.86
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 MOLECULAR REPLACEMENT FREE R-VALUE 1.6 38.48 1.37 41950 2082 99.61 0.1593 0.1578 0.1574 0.1868 0.1857 26.31
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 14.8005 f_angle_d 0.8098 f_chiral_restr 0.0489 f_plane_restr 0.0096 f_bond_d 0.0047
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2628 Nucleic Acid Atoms Solvent Atoms 393 Heterogen Atoms 32
Software Software Software Name Purpose PHENIX refinement DIALS data reduction DIALS data scaling PHENIX phasing