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Crystal Structure of human Tryptophan 2,3-dioxygenase in complex with PPN3 inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6PYZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 298 50 mM Sodium Citrate pH 5.6, 2.0% Tacsimate pH 5.0, 5.0% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.72 54.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 143.818 α = 90 b = 154.732 β = 90 c = 88.407 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 PILATUS3 S 6M 2023-02-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID 0.979320 APS 31-ID
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 2.05 154.73 99.6 0.033 0.042 0.026 1 17.4 4.6 123530
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 2.05 2.09 1.493 1.906 1.173 0.428 4.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.05 105.564 123459 6077 99.512 0.193 0.1914 0.1997 0.2176 0.2245 79.008
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] -2.341 -1.53 3.872
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 15.145 r_dihedral_angle_6_deg 13.406 r_dihedral_angle_3_deg 13.32 r_lrange_other 12.519 r_lrange_it 12.516 r_scangle_it 8.843 r_scangle_other 8.843 r_mcangle_it 7.104 r_mcangle_other 7.104 r_scbond_it 6.143
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 15.145 r_dihedral_angle_6_deg 13.406 r_dihedral_angle_3_deg 13.32 r_lrange_other 12.519 r_lrange_it 12.516 r_scangle_it 8.843 r_scangle_other 8.843 r_mcangle_it 7.104 r_mcangle_other 7.104 r_scbond_it 6.143 r_scbond_other 6.142 r_mcbond_other 5.059 r_mcbond_it 5.058 r_dihedral_angle_1_deg 4.657 r_angle_refined_deg 1.612 r_angle_other_deg 0.559 r_symmetry_nbd_refined 0.252 r_nbd_other 0.248 r_nbd_refined 0.236 r_nbtor_refined 0.189 r_symmetry_nbd_other 0.182 r_xyhbond_nbd_refined 0.141 r_symmetry_xyhbond_nbd_refined 0.125 r_ncsr_local_group_6 0.124 r_ncsr_local_group_4 0.119 r_ncsr_local_group_5 0.115 r_ncsr_local_group_3 0.114 r_ncsr_local_group_2 0.113 r_ncsr_local_group_1 0.108 r_chiral_restr 0.078 r_symmetry_nbtor_other 0.071 r_symmetry_xyhbond_nbd_other 0.037 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_gen_planes_other 0.004 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11724 Nucleic Acid Atoms Solvent Atoms 146 Heterogen Atoms 336
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction Aimless data scaling PHASER phasing