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BesD with Fe(II), chloride, and alpha-ketoglutarate
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 277 1:1 volume of protein solution (10 mg/mL BesD, lysine (1.5 mM), alpha-ketoglutarate (3 mM, pH 7)) and reservoir solution (MES pH 6.5 (100 mM), sodium chloride (0.6 mM), containing 20% (v/v) PEG 4000. Soaked anaerobically in a solution containing (NH4)2Fe(SO4)2 * 6H2O (1mM), alpha-ketoglutarate (1 mM), sodium ascorbate (1 mM), lysine (1 mM), and glycerol (20% (v/v) for 30 min before flash freezing in liquid nitrogen
Crystal Properties Matthews coefficient Solvent content 2.37 48.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.358 α = 115.36 b = 68.916 β = 91.57 c = 79.702 γ = 112.95
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 194 PIXEL DECTRIS PILATUS3 S 6M 2018-05-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 1.11 ALS 8.3.1
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 1.95 70.03 97.35 0.998 10.7 13.6 149915
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 1.95 2.02 95.7 0.78
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 SAD FREE R-VALUE 1.95 70.027 1.96 149912 7295 97.35 0.1791 0.1772 0.1812 0.2159 0.2187
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 18.977 f_angle_d 0.982 f_chiral_restr 0.058 f_bond_d 0.01 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7808 Nucleic Acid Atoms Solvent Atoms 847 Heterogen Atoms 89
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling CRANK2 phasing