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Crystal structure of L-Kynurenine in the active site of human Indoleamine-2,3-dioxygenase 1 (hIDO1)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7NGE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.2 293 Well : 0.1M Phosphate buffer, pH= 6.2, PEG 3350 = 16%
Protein: 5mM Hepes, 200mM NaCl, 5mM DTT
Crystal Properties Matthews coefficient Solvent content 2.83 56.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81 α = 90 b = 116.28 β = 90 c = 217.59 γ = 90
Symmetry Space Group P 21 21 2
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 channel-cut 2021-07-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 2 0.980 SOLEIL PROXIMA 2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.56 47.23 99.18 0.09638 0.998 13.33 13.6 66614 42.15
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.562 2.654 93.96 0.5299 0.855 2.22
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 FREE R-VALUE 7NGE 2.56 47.23 1.34 66418 3316 99.21 0.1834 0.1802 0.1817 0.2441 0.2446 46.4
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 12.1939 f_angle_d 0.9793 f_chiral_restr 0.0494 f_bond_d 0.0087 f_plane_restr 0.0077
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11813 Nucleic Acid Atoms Solvent Atoms 904 Heterogen Atoms 326
Software Software Software Name Purpose XDS data reduction PHENIX refinement MxCuBE data collection XSCALE data scaling PHASER phasing Coot model building