6PYY

Crystal Structure of human Tryptophan 2,3-dioxygenase in complex with PF-06840003 in Active Site and Exo 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
2.754.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 144.188α = 90
b = 154.037β = 90
c = 87.973γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX225HE2018-03-21MSINGLE 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
12.429.999.917.87.27724353.3
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)
12.42.530.391.4

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 REPLACEMENTTHROUGHOUT5TI92.429.973364377699.810.19340.19110.2375RANDOM53.319
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]
0.270.12-0.39
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.176
r_dihedral_angle_3_deg16.749
r_dihedral_angle_4_deg16.532
r_dihedral_angle_1_deg5.819
r_angle_refined_deg1.692
r_angle_other_deg1.285
r_chiral_restr0.072
r_bond_refined_d0.008
r_gen_planes_refined0.007
r_gen_planes_other0.003
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.176
r_dihedral_angle_3_deg16.749
r_dihedral_angle_4_deg16.532
r_dihedral_angle_1_deg5.819
r_angle_refined_deg1.692
r_angle_other_deg1.285
r_chiral_restr0.072
r_bond_refined_d0.008
r_gen_planes_refined0.007
r_gen_planes_other0.003
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms11436
Nucleic Acid Atoms
Solvent Atoms412
Heterogen Atoms308

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
SCALAdata scaling
PHASERphasing