6PYZ

Crystal Structure of human Tryptophan 2,3-dioxygenase in complex with PF-06840003 in Active Site


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5TI9 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1MICROBATCH29850 mM Sodium Citrate (pH 5.6), 2% Tacsimate (pH 5.0) 5% PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.9658.48

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 143.648α = 90
b = 154.158β = 90
c = 87.951γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX225HE2018-07-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 31-ID0.97931APS31-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)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
12.0229.8699.5111.37.512754450.4
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.022.1399.10.391.17.5

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 REPLACEMENTTHROUGHOUT5TI92.0229.86121109638099.320.19190.18930.2428RANDOM50.459
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]
-1.53-0.141.67
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.043
r_dihedral_angle_3_deg16.958
r_dihedral_angle_4_deg15.739
r_dihedral_angle_1_deg5.501
r_angle_refined_deg1.355
r_angle_other_deg1.287
r_chiral_restr0.066
r_gen_planes_refined0.006
r_bond_refined_d0.005
r_gen_planes_other0.003
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.043
r_dihedral_angle_3_deg16.958
r_dihedral_angle_4_deg15.739
r_dihedral_angle_1_deg5.501
r_angle_refined_deg1.355
r_angle_other_deg1.287
r_chiral_restr0.066
r_gen_planes_refined0.006
r_bond_refined_d0.005
r_gen_planes_other0.003
r_bond_other_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms11593
Nucleic Acid Atoms
Solvent Atoms1074
Heterogen Atoms304

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
SCALAdata scaling
PHASERphasing