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Crystal structure of L-Trp/Indoleamine 2,3-dioxygenagse 1 (hIDO1) complex with the JK-loop refined in the closed 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 6 293 15.4% PEG 3350
0.1M Phosphate buffer pH 6.0
Protein : 5mM HEPES pH 7.4, 200mM NaCl, 5mM DTT
Crystal Properties Matthews coefficient Solvent content 3.04 59.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.36 α = 90 b = 114.67 β = 90 c = 219.67 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 0.979 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 2.3 46.87 99.56 0.2072 0.217 0.06342 0.998 10.43 12.2 91724 46.98
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.301 2.384 97.63 2.655 2.778 0.8097 0.541 0.97 11.6
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 2.3 46.87 1.33 91519 1958 99.59 0.2162 0.215 0.2159 0.2707 0.2706 54.55
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 16.8824 f_angle_d 1.1258 f_chiral_restr 0.0561 f_bond_d 0.0095 f_plane_restr 0.0066
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11834 Nucleic Acid Atoms Solvent Atoms 668 Heterogen Atoms 481
Software Software Software Name Purpose PHENIX refinement XDS data reduction STARANISO data scaling PHASER phasing Coot model building MxCuBE data collection