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Structure of dithionite-reduced SidA ornithine hydroxylase with the FAD "in" and complexed with L-ornithine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4B63
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.5 293 Enzyme stock solution: 8-10 mg/mL SidA in 25 mM HEPES (pH 7.5) and 100 mM NaCl. Crystallization reservoir: 17-21 % PEG-3350, 0.1 M HEPES (pH 7.5), 0.1 M calcium acetate. Cryo-buffer: 15 % PEG-200, 20 % PEG 3350, 0.1 M HEPES (pH 7.5), 0.1 M calcium acetate, 50 mM L-ornithine, and 100 mM sodium dithionite
Crystal Properties Matthews coefficient Solvent content 2.67 54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.902 α = 90 b = 155.044 β = 91.01 c = 146.846 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 EIGER X 16M 2019-07-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.979180 APS 24-ID-E
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 2.23 155.04 97.6 0.209 0.239 0.113 0.986 7.8 4.5 225621
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 2.23 2.26 75.2 1.4 1.583 0.727 0.399 4.4
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 4B63 2.231 68.553 0.31 222906 11094 97.04 0.2332 0.2307 0.2326 0.2807 0.2819 57.4771
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 14.718 f_angle_d 1.029 f_chiral_restr 0.058 f_bond_d 0.008 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 27310 Nucleic Acid Atoms Solvent Atoms 383 Heterogen Atoms 425
Software Software Software Name Purpose Aimless data scaling PHENIX refinement PDB_EXTRACT data extraction XDS data reduction PHASER phasing