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Structure of the S167H mutant of human indoleamine 2,3 dioxygenase in complex with tryptophan and cyanide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2D0T PDB entry 2D0T
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 10 277 0.1 M sodium thiosulfate, 0.1 M CAPS, pH 10, 20% PEG8000
Crystal Properties Matthews coefficient Solvent content 2.88 57.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.91 α = 90 b = 97.95 β = 90 c = 129.34 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 2016-03-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 1.18076 SSRL BL9-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) 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 2.49 30 100 0.093 0.037 12 8.2 39398
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 2.49 2.59 100 2.96 1.18 0.497 0.8 8.3
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 PDB entry 2D0T 2.49 30 37294 1993 99.79 0.20368 0.2012 0.24955 0.2366 RANDOM 90.902
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] 1.08 -5.11 4.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.202 r_dihedral_angle_4_deg 14.239 r_dihedral_angle_3_deg 13.471 r_long_range_B_refined 7.496 r_long_range_B_other 7.496 r_dihedral_angle_1_deg 5.467 r_mcangle_it 5.095 r_mcangle_other 5.094 r_scangle_other 4.606 r_mcbond_it 3.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.202 r_dihedral_angle_4_deg 14.239 r_dihedral_angle_3_deg 13.471 r_long_range_B_refined 7.496 r_long_range_B_other 7.496 r_dihedral_angle_1_deg 5.467 r_mcangle_it 5.095 r_mcangle_other 5.094 r_scangle_other 4.606 r_mcbond_it 3.11 r_mcbond_other 3.103 r_scbond_it 2.749 r_scbond_other 2.749 r_angle_refined_deg 1.146 r_angle_other_deg 0.894 r_chiral_restr 0.073 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 r_gen_planes_other 0.002 r_bond_other_d 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 6004 Nucleic Acid Atoms Solvent Atoms 219 Heterogen Atoms 120
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing