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Crystal Structure of human Indoleamine 2,3-Dioxygenase 1 in complex with PF-06840003 in Active Site and Si site
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5WMU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 10 277 100 mM Sodium thiosulfate, 100 mM CAPS buffer pH 10.0, and 20% (w/v) PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.95 58.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.479 α = 90 b = 97.858 β = 90 c = 131.966 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 CCD RAYONIX MX225HE 2018-02-19 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 2.65 78.61 99.8 0.99 7.4 7.1 33561
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 2.65 2.79 100 0.54 1
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5WMU 2.65 40 31777 1671 99.61 0.2225 0.2201 0.2698 0.263 RANDOM 83.542
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] -1.76 -3.47 5.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.511 r_dihedral_angle_3_deg 18.762 r_dihedral_angle_4_deg 18.19 r_dihedral_angle_1_deg 6.477 r_angle_refined_deg 1.416 r_angle_other_deg 1.088 r_chiral_restr 0.052 r_gen_planes_refined 0.004 r_bond_refined_d 0.003 r_gen_planes_other 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.511 r_dihedral_angle_3_deg 18.762 r_dihedral_angle_4_deg 18.19 r_dihedral_angle_1_deg 6.477 r_angle_refined_deg 1.416 r_angle_other_deg 1.088 r_chiral_restr 0.052 r_gen_planes_refined 0.004 r_bond_refined_d 0.003 r_gen_planes_other 0.003 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5963 Nucleic Acid Atoms Solvent Atoms 188 Heterogen Atoms 167
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction SCALA data scaling PHASER phasing