5WN8

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
1MICROBATCH9.5277100 mM Sodium thiosulfate, 100 mM CAPS buffer pH 9.5, and 20% (w/v) PEG 8000
Crystal Properties
Matthews coefficientSolvent content
3.0159.1

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 86.735α = 90
b = 97.785β = 90
c = 128.739γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX225HE2017-03-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 31-ID0.91988APS31-ID

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
12.529.6999.90.0870.0230.5922.514.838582
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)
12.52.5651002.30.610.591.314.9

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 REPLACEMENTTHROUGHOUT2D0T2.529.6936596192899.840.215350.213470.25182RANDOM80.291
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]
-1.36-2.053.42
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.929
r_dihedral_angle_3_deg13.598
r_dihedral_angle_4_deg11.626
r_long_range_B_refined8.344
r_long_range_B_other8.332
r_dihedral_angle_1_deg5.233
r_mcangle_it3.484
r_mcangle_other3.483
r_scangle_other3.397
r_mcbond_it2.077
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.929
r_dihedral_angle_3_deg13.598
r_dihedral_angle_4_deg11.626
r_long_range_B_refined8.344
r_long_range_B_other8.332
r_dihedral_angle_1_deg5.233
r_mcangle_it3.484
r_mcangle_other3.483
r_scangle_other3.397
r_mcbond_it2.077
r_mcbond_other2.076
r_scbond_it1.992
r_scbond_other1.992
r_angle_refined_deg1.199
r_angle_other_deg0.872
r_chiral_restr0.068
r_bond_refined_d0.007
r_gen_planes_refined0.005
r_gen_planes_other0.003
r_bond_other_d0.001
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 Atoms5880
Nucleic Acid Atoms
Solvent Atoms148
Heterogen Atoms136

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing