☰ Navigation Tabs
Crystal Structure of human Tryptophan 2,3-dioxygenase in complex with PAN1 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 2.71 54.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 143.61 α = 90 b = 154.014 β = 90 c = 88.58 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 EIGER X 16M 2024-02-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-2 0.97934 NSLS-II 17-ID-2
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 2.648 34.29 92.7 0.1074 0.1207 0.0541 0.998 10.89 4.83 36145
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) 2.648 3.006 62.2 0.8788 0.9814 0.4322 0.611 1.84 5.1 1808
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 2.65 34.29 36137 1788 62.493 0.192 0.1899 0.1936 0.2344 0.2351 72.776
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] 1.588 -0.576 -1.013
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 21.05 r_dihedral_angle_3_deg 14.342 r_dihedral_angle_6_deg 11.473 r_lrange_it 10.514 r_lrange_other 10.514 r_scangle_it 5.797 r_scangle_other 5.797 r_mcangle_it 5.161 r_mcangle_other 5.16 r_dihedral_angle_1_deg 4.962
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 21.05 r_dihedral_angle_3_deg 14.342 r_dihedral_angle_6_deg 11.473 r_lrange_it 10.514 r_lrange_other 10.514 r_scangle_it 5.797 r_scangle_other 5.797 r_mcangle_it 5.161 r_mcangle_other 5.16 r_dihedral_angle_1_deg 4.962 r_scbond_it 3.415 r_scbond_other 3.414 r_mcbond_it 3.088 r_mcbond_other 3.081 r_angle_refined_deg 1.402 r_angle_other_deg 0.489 r_nbd_refined 0.242 r_nbd_other 0.197 r_nbtor_refined 0.196 r_symmetry_nbd_other 0.193 r_symmetry_nbd_refined 0.155 r_xyhbond_nbd_refined 0.149 r_ncsr_local_group_4 0.119 r_ncsr_local_group_5 0.118 r_ncsr_local_group_6 0.117 r_ncsr_local_group_2 0.114 r_ncsr_local_group_3 0.113 r_ncsr_local_group_1 0.109 r_symmetry_xyhbond_nbd_refined 0.093 r_symmetry_nbtor_other 0.074 r_chiral_restr 0.063 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_gen_planes_other 0.004 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11616 Nucleic Acid Atoms Solvent Atoms 19 Heterogen Atoms 340
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction STARANISO data scaling PHASER phasing