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Structure of human indoleamine-2,3-dioxygenase 1 (hIDO1) with a complete JK loop
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6E43
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.25 293 14% IN PEG 3350, 0.1 M IN PHOSPHATE BUFFER AT A PH OF 6.25
PROTEIN : IN HEPES 5 MM AND NACL 200MM
CRYOPROTECTION IN 20% OF GLYCEROL AND 20 MM OF SODIUM DITHIONITE, PH 7.6
Crystal Properties Matthews coefficient Solvent content 2.83 56.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.96 α = 90 b = 117.95 β = 90 c = 216.41 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 2019-11-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.979 SOLEIL PROXIMA 1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 2.438 49.18 84 0.1677 0.1742 0.998 8.81 13 77982 38.98
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.438 2.525 98 1.828 1.907 0.753 0.84 12.4
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 6E43 2.43796448682 49.1760318032 0.00224499941129 65724 3301 84.115953158 0.214105983061 0.211611041463 0.2127 0.257286553269 0.2604 39.8337568823
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 15.820795227 f_angle_d 1.04777832308 f_chiral_restr 0.0602284113232 f_bond_d 0.0136154282757 f_plane_restr 0.00713726166949
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12178 Nucleic Acid Atoms Solvent Atoms 695 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement Coot model building XDS data reduction PHASER phasing MxCuBE data collection XSCALE data scaling