6CXU

Structure of the S167H mutant of human indoleamine 2,3 dioxygenase in complex with tryptophan and cyanide


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2D0TPDB entry 2D0T

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1BATCH MODE102770.1 M sodium thiosulfate, 0.1 M CAPS, pH 10, 20% PEG8000
Crystal Properties
Matthews coefficientSolvent content
2.8857.24

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 86.91α = 90
b = 97.95β = 90
c = 129.34γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6Mmirror2016-03-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL9-21.18076SSRLBL9-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)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
12.49301000.0930.037128.239398
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)
12.492.591002.961.180.4970.88.3

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 REPLACEMENTTHROUGHOUTPDB entry 2D0T2.493037294199399.790.203680.20120.24955RANDOM90.902
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]
1.08-5.114.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.202
r_dihedral_angle_4_deg14.239
r_dihedral_angle_3_deg13.471
r_long_range_B_refined7.496
r_long_range_B_other7.496
r_dihedral_angle_1_deg5.467
r_mcangle_it5.095
r_mcangle_other5.094
r_scangle_other4.606
r_mcbond_it3.11
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.202
r_dihedral_angle_4_deg14.239
r_dihedral_angle_3_deg13.471
r_long_range_B_refined7.496
r_long_range_B_other7.496
r_dihedral_angle_1_deg5.467
r_mcangle_it5.095
r_mcangle_other5.094
r_scangle_other4.606
r_mcbond_it3.11
r_mcbond_other3.103
r_scbond_it2.749
r_scbond_other2.749
r_angle_refined_deg1.146
r_angle_other_deg0.894
r_chiral_restr0.073
r_bond_refined_d0.007
r_gen_planes_refined0.004
r_gen_planes_other0.002
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 Atoms6004
Nucleic Acid Atoms
Solvent Atoms219
Heterogen Atoms120

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing