5WMU

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


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1MICROBATCH10277.15100 mM Sodium thiosulfate, 100 mM pH 10.0 CAPS buffer, 20% (w/v) PEG 8000)
Crystal Properties
Matthews coefficientSolvent content
3.0259.29

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 89.301α = 90
b = 97.768β = 90
c = 125.643γ = 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
12.438.799.80.0460.022117.46437481
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)
12.42.4698.31.080.520.71.66

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 REPLACEMENTTHROUGHOUT2D0T2.438.6541644199499.610.216040.214040.25791RANDOM76.791
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]
-2.11-3.295.4
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.313
r_dihedral_angle_4_deg14.393
r_dihedral_angle_3_deg13.126
r_long_range_B_refined5.251
r_dihedral_angle_1_deg5.246
r_long_range_B_other5.209
r_mcangle_it3.25
r_mcangle_other3.25
r_scangle_other2.855
r_mcbond_it1.905
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.313
r_dihedral_angle_4_deg14.393
r_dihedral_angle_3_deg13.126
r_long_range_B_refined5.251
r_dihedral_angle_1_deg5.246
r_long_range_B_other5.209
r_mcangle_it3.25
r_mcangle_other3.25
r_scangle_other2.855
r_mcbond_it1.905
r_mcbond_other1.905
r_scbond_it1.674
r_scbond_other1.674
r_angle_refined_deg1.074
r_angle_other_deg0.871
r_chiral_restr0.066
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 Atoms6002
Nucleic Acid Atoms
Solvent Atoms224
Heterogen Atoms120

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing