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Crystal Structure of human Tryptophan 2,3-dioxygenase in complex with PPN1 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 54.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 143.805 α = 90 b = 154.925 β = 90 c = 88.32 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 2.05 154.93 99.5 0.043 0.051 0.027 0.999 17.1 6.7 123426
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 1.808 2.168 1.172 0.404 6.1
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 2.05 105.62 123356 6093 99.412 0.195 0.1942 0.2018 0.2154 0.2206 79.722
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] -2.349 -1.453 3.801
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 18.426 r_dihedral_angle_3_deg 13.36 r_dihedral_angle_6_deg 12.965 r_lrange_other 10.97 r_lrange_it 10.968 r_scangle_it 7.214 r_scangle_other 7.214 r_mcangle_it 5.809 r_mcangle_other 5.809 r_scbond_it 4.93
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 18.426 r_dihedral_angle_3_deg 13.36 r_dihedral_angle_6_deg 12.965 r_lrange_other 10.97 r_lrange_it 10.968 r_scangle_it 7.214 r_scangle_other 7.214 r_mcangle_it 5.809 r_mcangle_other 5.809 r_scbond_it 4.93 r_scbond_other 4.93 r_dihedral_angle_1_deg 4.67 r_mcbond_it 4.045 r_mcbond_other 4.033 r_angle_refined_deg 1.468 r_angle_other_deg 0.509 r_nbd_other 0.272 r_nbd_refined 0.233 r_symmetry_nbd_refined 0.207 r_nbtor_refined 0.187 r_symmetry_nbd_other 0.182 r_symmetry_xyhbond_nbd_refined 0.153 r_xyhbond_nbd_refined 0.14 r_ncsr_local_group_6 0.116 r_ncsr_local_group_2 0.114 r_ncsr_local_group_4 0.104 r_ncsr_local_group_3 0.101 r_ncsr_local_group_5 0.099 r_ncsr_local_group_1 0.094 r_symmetry_nbtor_other 0.071 r_chiral_restr 0.068 r_symmetry_xyhbond_nbd_other 0.016 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_gen_planes_other 0.004 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11755 Nucleic Acid Atoms Solvent Atoms 125 Heterogen Atoms 336
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction Aimless data scaling PHASER phasing