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Mapping the binding trajectory of a suicide inhibitor in human indoleamine 2,3-dioxygenase 1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5WN8 PDB entry 5WN8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 10 277 100 mM sodium thiosulfate, 100 mM CAPS, pH 10.0, 200 mM sodium chloride, 20% w/v PEG8000
Crystal Properties Matthews coefficient Solvent content 3.01 59.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.604 α = 90 b = 96.565 β = 90 c = 130.764 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD RAYONIX MX225HE 2018-03-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID 0.97931 APS 31-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) 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 2.94 29.36 99.9 0.123 0.049 9.2 7.4 23694
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.94 3.1 100 2.043 0.795 0.33 1.1 7.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 5WN8 2.94 29.36 22499 1145 99.79 0.19301 0.19069 0.198 0.2399 0.2431 RANDOM 109.659
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] -3.03 0.53 2.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.746 r_dihedral_angle_3_deg 19.858 r_dihedral_angle_4_deg 16.62 r_long_range_B_refined 11.934 r_long_range_B_other 11.933 r_mcangle_it 8.466 r_mcangle_other 8.464 r_dihedral_angle_1_deg 8.206 r_scangle_other 7.78 r_mcbond_it 5.347
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.746 r_dihedral_angle_3_deg 19.858 r_dihedral_angle_4_deg 16.62 r_long_range_B_refined 11.934 r_long_range_B_other 11.933 r_mcangle_it 8.466 r_mcangle_other 8.464 r_dihedral_angle_1_deg 8.206 r_scangle_other 7.78 r_mcbond_it 5.347 r_mcbond_other 5.347 r_scbond_it 4.65 r_scbond_other 4.649 r_angle_other_deg 0.694 r_angle_refined_deg 0.515 r_chiral_restr 0.026 r_gen_planes_refined 0.007 r_gen_planes_other 0.005 r_bond_refined_d 0.002 r_bond_other_d 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5846 Nucleic Acid Atoms Solvent Atoms 120 Heterogen Atoms 108
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing