☰ Navigation Tabs
Crystal Structure of human Tryptophan 2,3-dioxygenase in complex with PYN1 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 2.69 54.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 142.959 α = 90 b = 154.17 β = 90 c = 88.277 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 2.624 34.291 93.7 0.1357 0.148 0.0582 0.998 9.62 6.38 31809
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) 2.624 2.997 77.1 1.0604 1.1417 0.42 0.647 1.79 7.31 1590
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 2.624 34.291 31808 1625 53.781 0.205 0.2023 0.2045 0.2583 0.2538 75.541
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] 1.094 -0.289 -0.805
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 18.277 r_dihedral_angle_3_deg 14.554 r_lrange_it 11.897 r_lrange_other 11.897 r_dihedral_angle_6_deg 10.713 r_scangle_it 6.086 r_scangle_other 6.085 r_mcangle_other 5.642 r_mcangle_it 5.641 r_dihedral_angle_1_deg 4.747
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 18.277 r_dihedral_angle_3_deg 14.554 r_lrange_it 11.897 r_lrange_other 11.897 r_dihedral_angle_6_deg 10.713 r_scangle_it 6.086 r_scangle_other 6.085 r_mcangle_other 5.642 r_mcangle_it 5.641 r_dihedral_angle_1_deg 4.747 r_scbond_it 3.628 r_scbond_other 3.624 r_mcbond_it 3.37 r_mcbond_other 3.365 r_angle_refined_deg 1.417 r_angle_other_deg 0.481 r_nbd_refined 0.241 r_symmetry_nbd_other 0.204 r_nbd_other 0.201 r_nbtor_refined 0.198 r_symmetry_nbd_refined 0.159 r_xyhbond_nbd_refined 0.149 r_symmetry_xyhbond_nbd_refined 0.148 r_ncsr_local_group_6 0.123 r_ncsr_local_group_4 0.121 r_ncsr_local_group_2 0.12 r_ncsr_local_group_5 0.12 r_ncsr_local_group_3 0.115 r_ncsr_local_group_1 0.112 r_symmetry_xyhbond_nbd_other 0.092 r_symmetry_nbtor_other 0.077 r_chiral_restr 0.06 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_gen_planes_other 0.003 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11596 Nucleic Acid Atoms Solvent Atoms 12 Heterogen Atoms 332
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction STARANISO data scaling PHASER phasing