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Crystal Structure of human Tryptophan 2,3-dioxygenase in complex with PAN3F 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 55.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 144.081 α = 90 b = 154.84 β = 90 c = 88.757 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 2.45 154.84 99.8 0.067 0.08 0.043 0.999 12.6 6.1 73492
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 2.45 2.5 1.33 1.607 0.887 0.484 5.3
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 2.45 77.54 73427 3662 99.686 0.202 0.1994 0.202 0.2442 0.242 91.048
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] -0.078 -3.826 3.905
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 14.482 r_lrange_other 14.482 r_dihedral_angle_2_deg 13.836 r_dihedral_angle_3_deg 13.805 r_dihedral_angle_6_deg 13.141 r_scangle_it 9.349 r_scangle_other 9.349 r_mcangle_it 8.18 r_mcangle_other 8.177 r_scbond_it 6.245
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 14.482 r_lrange_other 14.482 r_dihedral_angle_2_deg 13.836 r_dihedral_angle_3_deg 13.805 r_dihedral_angle_6_deg 13.141 r_scangle_it 9.349 r_scangle_other 9.349 r_mcangle_it 8.18 r_mcangle_other 8.177 r_scbond_it 6.245 r_scbond_other 6.245 r_mcbond_it 5.605 r_mcbond_other 5.588 r_dihedral_angle_1_deg 4.847 r_angle_refined_deg 1.556 r_angle_other_deg 0.543 r_symmetry_nbd_refined 0.339 r_nbd_refined 0.239 r_nbd_other 0.216 r_symmetry_xyhbond_nbd_refined 0.209 r_nbtor_refined 0.189 r_symmetry_nbd_other 0.185 r_xyhbond_nbd_refined 0.142 r_ncsr_local_group_6 0.122 r_ncsr_local_group_3 0.121 r_ncsr_local_group_5 0.121 r_ncsr_local_group_2 0.118 r_ncsr_local_group_4 0.118 r_ncsr_local_group_1 0.114 r_chiral_restr 0.076 r_symmetry_xyhbond_nbd_other 0.075 r_symmetry_nbtor_other 0.071 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 11675 Nucleic Acid Atoms Solvent Atoms 12 Heterogen Atoms 344
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction Aimless data scaling PHASER phasing