4U74

Crystal structure of 4-phenylimidazole bound form of human indoleamine 2,3-dioxygenase (G262A mutant)


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP9.129312 % (W/V) PEG 8000, 0.2 M ammonium acetate, 1 mM 4-phenylimidazole, 0.1 M CHES
Crystal Properties
Matthews coefficientSolvent content
3.160.27

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 85.884α = 90
b = 99.539β = 90
c = 132.343γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU JUPITER 210mirrors2009-02-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL26B11.00SPring-8BL26B1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
12.3401000.0790.07926.597.350474-327.9
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.32.381000.6850.6852.6916.9

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 REPLACEMENTTHROUGHOUT2D0T2.3119.8949175239396.970.17370.17130.2195RANDOM33.992
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]
-0.330.5-0.17
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.88
r_dihedral_angle_4_deg19.127
r_dihedral_angle_3_deg16.854
r_dihedral_angle_1_deg6.029
r_angle_refined_deg1.996
r_chiral_restr0.135
r_bond_refined_d0.019
r_gen_planes_refined0.011
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5938
Nucleic Acid Atoms
Solvent Atoms307
Heterogen Atoms160

Software

Software
Software NamePurpose
HKL-2000data reduction
PDB_EXTRACTdata extraction
REFMACrefinement
HKLdata scaling