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Crystal structure of human Indoleamine-2,3-dioxygenase 1 (hIDO1) with different conformations for G261-G265 fragment
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 6.2 298 Well: 0.1M KH2PO4/K2HPO4 buffer at pH 6.2 supplemented with 17% of PEG 3350 solution
Protein: 5 mM HEPES/NaOH pH 7.6, 200 mM NaCl, 5 mM DTT
Crystal Properties Matthews coefficient Solvent content 3 59.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.04 α = 90 b = 117.61 β = 90 c = 217.18 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 9M 2021-07-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 2 0.98011 SOLEIL PROXIMA 2
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 2.48 49.07 99.71 0.1683 0.1751 0.04815 0.998 11.01 13.3 73894 48.89
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.485 2.574 98.66 1.46 0.4084 0.802 1.73 13.5
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 2.48 49.07 1.35 73798 3694 99.74 0.1993 0.1963 0.197 0.2586 0.2584 54.24
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 10.2456 f_angle_d 1.0059 f_chiral_restr 0.049 f_bond_d 0.0086 f_plane_restr 0.0078
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11881 Nucleic Acid Atoms Solvent Atoms 686 Heterogen Atoms 228
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing MxCuBE data collection Coot model building