☰ Navigation Tabs
Crystal structure of the indoleamine 2,3-dioxygenagse 1 (IDO1) complexed with INCB14943
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5EK3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 9.5 293 10% (w/v) PEG-8000, 0.1M CHES pH 9.5, 0.2M NaCl
Crystal Properties Matthews coefficient Solvent content 3 58.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.05 α = 90 b = 97.38 β = 90 c = 128.47 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 PILATUS3 6M 2016-07-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.9785 SSRF BL19U1
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 3.2 97.38 98.4 0.145 0.157 0.057 0.991 8.7 6.7 18282
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 3.2 3.42 97.6 0.89 0.973 0.379 0.712 6 3212
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 5EK3 3.2 25 17190 931 97.33 0.23015 0.22781 0.2304 0.27432 0.2738 RANDOM 88.162
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] -0.52 -3.64 4.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.418 r_dihedral_angle_4_deg 21.311 r_dihedral_angle_3_deg 19.585 r_long_range_B_refined 6.077 r_long_range_B_other 6.077 r_dihedral_angle_1_deg 5.208 r_mcangle_it 1.902 r_mcangle_other 1.902 r_scangle_other 1.725 r_angle_refined_deg 1.465
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.418 r_dihedral_angle_4_deg 21.311 r_dihedral_angle_3_deg 19.585 r_long_range_B_refined 6.077 r_long_range_B_other 6.077 r_dihedral_angle_1_deg 5.208 r_mcangle_it 1.902 r_mcangle_other 1.902 r_scangle_other 1.725 r_angle_refined_deg 1.465 r_angle_other_deg 1.379 r_scbond_it 1.182 r_scbond_other 1.181 r_mcbond_it 1.087 r_mcbond_other 1.087 r_chiral_restr 0.085 r_gen_planes_refined 0.012 r_gen_planes_other 0.011 r_bond_refined_d 0.01 r_bond_other_d 0.007 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 5888 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 122
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction