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Crystal structure of human tryptophan 2,3-dioxygenase in complex with carbon monoxide and tryptophan
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5TI9 PDB entry 5TI9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 5 298 50 mM sodium citrate, pH 5.6, 2% Tacsimate, pH 5.0, 5% PEG3350
Crystal Properties Matthews coefficient Solvent content 2.97 58.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 144.725 α = 90 b = 154.493 β = 90 c = 88.306 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 CCD RAYONIX MX325HE 2016-04-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID 0.97931 APS 31-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.05 19.97 96.7 0.99 7.9 6.7 120121
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.05 2.16 0.59 1.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 5TI9 2.05 19.97 113859 6206 96.41 0.1846 0.1828 0.1898 0.2174 0.2234 RANDOM 37.501
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] -0.78 -0.45 1.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.319 r_dihedral_angle_4_deg 16.761 r_dihedral_angle_3_deg 14.645 r_dihedral_angle_1_deg 5.209 r_angle_refined_deg 1.232 r_angle_other_deg 1.196 r_chiral_restr 0.057 r_gen_planes_refined 0.005 r_bond_refined_d 0.004 r_gen_planes_other 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.319 r_dihedral_angle_4_deg 16.761 r_dihedral_angle_3_deg 14.645 r_dihedral_angle_1_deg 5.209 r_angle_refined_deg 1.232 r_angle_other_deg 1.196 r_chiral_restr 0.057 r_gen_planes_refined 0.005 r_bond_refined_d 0.004 r_gen_planes_other 0.003 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11632 Nucleic Acid Atoms Solvent Atoms 773 Heterogen Atoms 300
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction SCALA data scaling PHASER phasing