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Crystal structure of L-Trp/Indoleamine 2,3-dioxygenase (hIDO1) complex with the JK-loop refined in the intermediate 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 6 298 0.1M Phosphate buffer
15.4% PEG 3350
Protein buffer : 5mM Hepes, 200 mM NaCl, 5 mM DTT
Cryoprotection : 20% glycerol, 20 mM sodium dithionite
Crystal Properties Matthews coefficient Solvent content 2.81 56.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.89 α = 90 b = 115.72 β = 90 c = 217.53 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 49.22 99.65 0.997 7.21 7.21 71454 54.62
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 2.5 2.589 99.42 0.59 0.79
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 49.22 1.34 71321 3562 99.43 0.2213 0.218 0.2185 0.2851 0.2839 61.98
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 18.8489 f_angle_d 1.0819 f_chiral_restr 0.0516 f_plane_restr 0.01 f_bond_d 0.0095
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11891 Nucleic Acid Atoms Solvent Atoms 497 Heterogen Atoms 362
Software Software Software Name Purpose PHENIX refinement PDB_EXTRACT data extraction MxCuBE data collection XDS data reduction Coot model building PHASER phasing XDS data scaling