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Crystal structure of human indoleamine 2,3-dioxygenase bound to a triazole inhibitor and alanine molecule.
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 VAPOR DIFFUSION, SITTING DROP 8.5 298 27-33% PEG 8000/Ethylene glycol mix
100mM Tris/Bicine mix pH 8.5
20-40mM L-alanine
Crystal Properties Matthews coefficient Solvent content 3.1 60.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.48 α = 90 b = 96.89 β = 90 c = 132.19 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 2012-05-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9763 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim 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 2.26 71.78 98.6 0.062 14 3.6 51328 52.54
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.26 2.32 98.2 0.714 1.9 3.8
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 (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 2.26 71.78 51268 2600 98.38 0.1925 0.1908 0.1986 0.225 0.2333 RANDOM 56.12
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] 17.8263 -3.0646 -14.7617
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 20.24 t_omega_torsion 2.69 t_angle_deg 1.04 t_bond_d 0.009 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 20.24 t_omega_torsion 2.69 t_angle_deg 1.04 t_bond_d 0.009 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_pseud_angle t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6023 Nucleic Acid Atoms Solvent Atoms 217 Heterogen Atoms 138
Software Software Software Name Purpose xia2 data scaling BUSTER refinement PDB_EXTRACT data extraction xia2 data reduction MOLREP phasing