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Crystal structure of the indoleamine 2,3-dioxygenagse 2 (IDO2) complexed with 5-methoxy-L-Trp
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other IDO2 5MeO-L-Trp complex
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 277 PEG 3350, Sodium citrate tribasic dihydrate
Crystal Properties Matthews coefficient Solvent content 6.15 80
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 198.253 α = 90 b = 198.253 β = 90 c = 94.113 γ = 120
Symmetry Space Group P 31 2 1
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 2025-01-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.9 SPring-8 BL44XU
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 49.56 99.9 0.999 15.1 7 73530
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 2.55 0.525
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.5 45.38 1.35 73497 3820 99.87 0.2481 0.2464 0.2465 0.2801 0.2801
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 18.443 f_angle_d 1.172 f_chiral_restr 0.163 f_bond_d 0.011 f_plane_restr 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5861 Nucleic Acid Atoms Solvent Atoms 105 Heterogen Atoms 133
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling MOLREP phasing