☰ Navigation Tabs
Structural Insights into Substrate and Inhibitor Binding Sites in Human Indoleamine 2,3-Dioxygenase 1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2D0T
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 10 277 100 mM Sodium thiosulfate, 100 mM pH 10.0 CAPS buffer, and 20% (w/v) PEG 8000
Crystal Properties Matthews coefficient Solvent content 3.05 59.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.057 α = 90 b = 97.566 β = 90 c = 130.416 γ = 90
Symmetry Space Group P 21 21 21
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 mirror 2016-03-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.9794 SSRL BL9-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.69 39.1 99.6 0.068 0.033 1 12.8 5.9 31517
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.69 2.76 98.3 1.75 0.85 0.44 0.9 6
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 2D0T 2.69 39.1 29358 1988 99.11 0.21698 0.21448 0.2136 0.25415 0.2535 RANDOM 99.372
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] 0.16 -3.47 3.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.641 r_dihedral_angle_4_deg 12.549 r_dihedral_angle_3_deg 12.385 r_dihedral_angle_1_deg 5.034 r_long_range_B_refined 3.601 r_long_range_B_other 3.595 r_mcangle_it 1.528 r_mcangle_other 1.528 r_scangle_other 1.125 r_angle_refined_deg 1.042
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.641 r_dihedral_angle_4_deg 12.549 r_dihedral_angle_3_deg 12.385 r_dihedral_angle_1_deg 5.034 r_long_range_B_refined 3.601 r_long_range_B_other 3.595 r_mcangle_it 1.528 r_mcangle_other 1.528 r_scangle_other 1.125 r_angle_refined_deg 1.042 r_angle_other_deg 0.853 r_mcbond_it 0.839 r_mcbond_other 0.839 r_scbond_it 0.65 r_scbond_other 0.65 r_chiral_restr 0.067 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5988 Nucleic Acid Atoms Solvent Atoms 131 Heterogen Atoms 144
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing