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Crystal structure of L-Trp/Indoleamine 2,3-dioxygenagse 1 (hIDO1) complex with the JK-loop refined in the open conformation
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7A62
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.4 298 14.5% PEG 3350
0.1M Phosphate buffer
2mM L-Trp
Protein buffer : Hepes 5mM, 200mM NaCl, 5mM DTT
Cryoprotection: 20 mM sodium dithionite, 20% glycerol
Crystal Properties Matthews coefficient Solvent content 2.81 56.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.36 α = 90 b = 114.57 β = 90 c = 220.98 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 EIGER2 X 9M 2020-07-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 2 0.98012 SOLEIL PROXIMA 2
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 2.5 49.29 99.34 0.995 6.7 7 71786 52.26
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 2.504 2.593 97.88 0.606 0.95
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 7A62 2.5 49.29 1.34 71579 3582 99.37 0.2182 0.2151 0.216 0.2788 0.2762 58.73
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 19.2593 f_angle_d 1.1214 f_chiral_restr 0.053 f_bond_d 0.0088 f_plane_restr 0.0084
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11782 Nucleic Acid Atoms Solvent Atoms 492 Heterogen Atoms 429
Software Software Software Name Purpose PHENIX refinement MxCuBE data collection Coot model building PHASER phasing XDS data reduction XDS data scaling