5WMX

Structural Insights into Substrate and Inhibitor Binding Sites in Human Indoleamine 2,3-Dioxygenase 1


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2D0T 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1MICROBATCH10277100 mM Sodium thiosulfate, 100 mM pH 10.0 CAPS buffer, and 20% (w/v) PEG 8000
Crystal Properties
Matthews coefficientSolvent content
3.0559.68

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 87.057α = 90
b = 97.566β = 90
c = 130.416γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6Mmirror2016-03-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL9-20.9794SSRLBL9-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.6939.199.60.0680.033112.85.931517
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)RedundancyNumber Unique Reflections (All)
12.692.7698.31.750.850.440.96

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2D0T2.6939.129358198899.110.216980.214480.25415RANDOM99.372
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]
0.16-3.473.32
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.641
r_dihedral_angle_4_deg12.549
r_dihedral_angle_3_deg12.385
r_dihedral_angle_1_deg5.034
r_long_range_B_refined3.601
r_long_range_B_other3.595
r_mcangle_it1.528
r_mcangle_other1.528
r_scangle_other1.125
r_angle_refined_deg1.042
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.641
r_dihedral_angle_4_deg12.549
r_dihedral_angle_3_deg12.385
r_dihedral_angle_1_deg5.034
r_long_range_B_refined3.601
r_long_range_B_other3.595
r_mcangle_it1.528
r_mcangle_other1.528
r_scangle_other1.125
r_angle_refined_deg1.042
r_angle_other_deg0.853
r_mcbond_it0.839
r_mcbond_other0.839
r_scbond_it0.65
r_scbond_other0.65
r_chiral_restr0.067
r_bond_refined_d0.007
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
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 AtomsNumber
Protein Atoms5988
Nucleic Acid Atoms
Solvent Atoms131
Heterogen Atoms144

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing