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Apo-form of Human Tryptophan 2,3-Dioxygenase Induced by NADH Binding
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6PYZ 6PYZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 5.6 293 50 mM Sodium Citrate, pH 5.6
2% Tacsimate
PEG 3350 (4-12%)
Crystal Properties Matthews coefficient Solvent content 2.77 55.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 143.855 α = 90 b = 156.264 β = 90 c = 88.986 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 PILATUS 6M Rh coated flat bent M0, toroidal focusing post-monochromator M1 2021-11-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 1.549750 SSRL BL9-2
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 3.18 19.974 99.5 0.098 0.106 0.04 1 18.5 12.9 34269
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 3.18 3.34 2.888 3.115 1.163 0.644 13.8
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6PYZ 3.18 19.974 34173 1774 99.199 0.246 0.2441 0.2453 0.2783 0.2844 106.154
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] 4.274 -0.966 -3.308
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.81 r_dihedral_angle_3_deg 15.577 r_lrange_it 13.605 r_lrange_other 13.605 r_dihedral_angle_4_deg 8.111 r_mcangle_it 7.57 r_mcangle_other 7.57 r_scangle_it 7.336 r_scangle_other 7.335 r_dihedral_angle_1_deg 4.737
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.81 r_dihedral_angle_3_deg 15.577 r_lrange_it 13.605 r_lrange_other 13.605 r_dihedral_angle_4_deg 8.111 r_mcangle_it 7.57 r_mcangle_other 7.57 r_scangle_it 7.336 r_scangle_other 7.335 r_dihedral_angle_1_deg 4.737 r_mcbond_it 4.702 r_mcbond_other 4.702 r_scbond_it 4.457 r_scbond_other 4.455 r_angle_refined_deg 1.276 r_angle_other_deg 1.24 r_nbd_other 0.302 r_nbd_refined 0.242 r_symmetry_nbd_refined 0.195 r_symmetry_nbd_other 0.192 r_nbtor_refined 0.165 r_ncsr_local_group_5 0.136 r_xyhbond_nbd_refined 0.133 r_ncsr_local_group_1 0.129 r_ncsr_local_group_2 0.124 r_ncsr_local_group_3 0.122 r_ncsr_local_group_6 0.119 r_ncsr_local_group_4 0.111 r_symmetry_nbtor_other 0.078 r_chiral_restr 0.05 r_gen_planes_refined 0.005 r_bond_refined_d 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9040 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 64
Software Software Software Name Purpose REFMAC refinement REFMAC refinement Coot model building Aimless data scaling PHASER phasing XDS data reduction