6E35

Crystal structure of human indoleamime 2,3-dioxygenase (IDO1) in complex with L-Trp and cyanide, Northeast Structural Genomics Target HR6160


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1MICROBATCH5277Protein solution: IDO1 (45 mg/ml), 10 mM IDE, 1.5 mM L-Trp, 5 mM KCN in 10 mM MES (pH 6.5), and 25 mM NaCl. Precipitation Reagent: 20% (W/V) PEG 4000, 0.1 M Sodium Acetate (pH 5), and 0.1 M Ammonium chloride.
Crystal Properties
Matthews coefficientSolvent content
2.956

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 85.77α = 90
b = 90.302β = 90
c = 136.766γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2012-09-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X4C0.97885NSLSX4C

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
12.41140.69794.70.127.412.93895645
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.4112.4999.50.592.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE2D0T2.41140.6971.3438956388293.430.18760.18210.2356
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]
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d18.078
f_angle_d1.159
f_chiral_restr0.059
f_bond_d0.011
f_plane_restr0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5781
Nucleic Acid Atoms
Solvent Atoms233
Heterogen Atoms132

Software

Software
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
COMOphasing