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Crystal structure of a photochemical intermediate of human indoleamine 2,3-dioxygenase 1 in complex with carbon monoxide and tryptophan
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5WMU PDB entry 5WMU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 10 277 100 mM sodium thiosulfate, 100 mM CAPS, pH 10.0, 20% w/v PEG8000
Crystal Properties Matthews coefficient Solvent content 2.9 57.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.944 α = 90 b = 97.727 β = 90 c = 130.628 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 EIGER X 16M 2019-05-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-2 0.97931 NSLS-II 17-ID-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.95 29.34 99.9 0.098 1 12.2 7.6 24106
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.95 3.13 100 2.015 0.53 1.2 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 PDB entry 5WMU 2.95 29.34 22893 1165 99.85 0.2175 0.2152 0.2155 0.2641 0.269 RANDOM 102.551
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] -1.87 -3.07 4.94
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.747 r_dihedral_angle_3_deg 18.455 r_dihedral_angle_4_deg 14.062 r_dihedral_angle_1_deg 5.813 r_angle_refined_deg 1.229 r_angle_other_deg 1.034 r_chiral_restr 0.041 r_gen_planes_refined 0.003 r_gen_planes_other 0.003 r_bond_refined_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.747 r_dihedral_angle_3_deg 18.455 r_dihedral_angle_4_deg 14.062 r_dihedral_angle_1_deg 5.813 r_angle_refined_deg 1.229 r_angle_other_deg 1.034 r_chiral_restr 0.041 r_gen_planes_refined 0.003 r_gen_planes_other 0.003 r_bond_refined_d 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5932 Nucleic Acid Atoms Solvent Atoms 63 Heterogen Atoms 120
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction Aimless data scaling PHASER phasing