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Crystal Structure of human Tryptophan 2,3-dioxygenase in complex with PAN3 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 2.74 55.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 144.042 α = 90 b = 155.112 β = 90 c = 88.515 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 0.979300 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 2.25 155.11 99.9 0.058 0.069 0.037 0.999 12.7 6.5 94512
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 2.25 2.29 1.451 1.741 0.946 0.47 6.2
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 2.25 88.672 94450 4874 99.781 0.203 0.2015 0.2071 0.2233 0.2291 88.555
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] -1.138 0.045 1.093
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 15.353 r_dihedral_angle_3_deg 13.941 r_dihedral_angle_6_deg 13.932 r_lrange_it 13.025 r_lrange_other 13.025 r_scangle_it 8.937 r_scangle_other 8.937 r_mcangle_it 7.217 r_mcangle_other 7.216 r_scbond_it 6.051
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 15.353 r_dihedral_angle_3_deg 13.941 r_dihedral_angle_6_deg 13.932 r_lrange_it 13.025 r_lrange_other 13.025 r_scangle_it 8.937 r_scangle_other 8.937 r_mcangle_it 7.217 r_mcangle_other 7.216 r_scbond_it 6.051 r_scbond_other 6.051 r_mcbond_it 4.997 r_mcbond_other 4.992 r_dihedral_angle_1_deg 4.636 r_angle_refined_deg 1.529 r_angle_other_deg 0.537 r_symmetry_xyhbond_nbd_refined 0.276 r_symmetry_nbd_refined 0.263 r_nbd_other 0.254 r_nbd_refined 0.234 r_nbtor_refined 0.187 r_symmetry_nbd_other 0.183 r_xyhbond_nbd_refined 0.146 r_ncsr_local_group_6 0.126 r_ncsr_local_group_2 0.12 r_ncsr_local_group_4 0.116 r_ncsr_local_group_5 0.116 r_ncsr_local_group_1 0.112 r_ncsr_local_group_3 0.11 r_chiral_restr 0.072 r_symmetry_nbtor_other 0.07 r_symmetry_xyhbond_nbd_other 0.07 r_bond_refined_d 0.008 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 11644 Nucleic Acid Atoms Solvent Atoms 23 Heterogen Atoms 340
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction Aimless data scaling PHASER phasing