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Crystal structure of OhyA(E82A)-18:1/h18:0-FAD complex from Staphylococcus aureus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7KAV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293.15 Crystallized: 15% v/v PEG 3000, 200 mM magnesium chloride, 100 mM sodium cacodylate, pH 6.5; Crystals soaked in 15% PEG3000, 200 mM magnesium chloride, 100 mM sodium cacodylate, pH 6.5, and 750 uM FAD. Cryo: 15% v/v PEG3000, 200 mM magnesium chloride, 100 mM sodium cacodylate, pH 6.5, 30% glycerol
Crystal Properties Matthews coefficient Solvent content 2.68 54.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 188.022 α = 90 b = 113.085 β = 116.91 c = 118.393 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 EIGER X 16M 2019-11-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.0 APS 22-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rpim I (All) 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 1.85 22.42 98.5 0.04 6.4 3.8 183821
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.85 1.9 96.3 0.485 3.8
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 7KAV 1.854 22.42 1.42 183776 2005 98.48 0.1942 0.1936 0.1996 0.2487 0.2526 29.2785
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 6.97 f_angle_d 1.162 f_chiral_restr 0.063 f_bond_d 0.014 f_plane_restr 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14099 Nucleic Acid Atoms Solvent Atoms 2725 Heterogen Atoms 331
Software Software Software Name Purpose PHENIX refinement PDB_EXTRACT data extraction KYLIN data reduction KYLIN data scaling PHASER phasing