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Crystal Structure of human Tryptophan 2,3-dioxygenase in complex with PYN3 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 54.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 143.804 α = 90 b = 154.754 β = 90 c = 88.254 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 2023-03-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID 0.979310 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 2.1 154.75 99.9 0.041 0.049 0.026 0.999 17.4 6.6 115256
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 2.1 2.14 1.528 1.803 0.948 0.477 7
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.1 88.41 115171 5857 99.871 0.205 0.2029 0.2339 0.2456 84.554
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] -1.706 -1.112 2.818
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 15.04 r_dihedral_angle_3_deg 13.195 r_dihedral_angle_6_deg 12.962 r_lrange_other 11.788 r_lrange_it 11.786 r_scangle_it 7.643 r_scangle_other 7.642 r_mcangle_it 6.338 r_mcangle_other 6.338 r_scbond_it 5.274
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 15.04 r_dihedral_angle_3_deg 13.195 r_dihedral_angle_6_deg 12.962 r_lrange_other 11.788 r_lrange_it 11.786 r_scangle_it 7.643 r_scangle_other 7.642 r_mcangle_it 6.338 r_mcangle_other 6.338 r_scbond_it 5.274 r_scbond_other 5.273 r_dihedral_angle_1_deg 4.715 r_mcbond_it 4.483 r_mcbond_other 4.482 r_angle_refined_deg 1.431 r_angle_other_deg 0.514 r_nbd_refined 0.237 r_symmetry_nbd_refined 0.221 r_nbd_other 0.203 r_nbtor_refined 0.188 r_symmetry_nbd_other 0.183 r_xyhbond_nbd_refined 0.136 r_symmetry_xyhbond_nbd_refined 0.134 r_ncsr_local_group_5 0.123 r_ncsr_local_group_6 0.12 r_ncsr_local_group_4 0.115 r_ncsr_local_group_1 0.114 r_ncsr_local_group_3 0.114 r_ncsr_local_group_2 0.113 r_chiral_restr 0.072 r_symmetry_nbtor_other 0.07 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 11618 Nucleic Acid Atoms Solvent Atoms 113 Heterogen Atoms 332
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction Aimless data scaling PHASER phasing