6PYZ | pdb_00006pyz

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)
Type	Source	Accession Code	Details
experimental model	PDB	5TI9

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROBATCH		298	50 mM Sodium Citrate (pH 5.6), 2% Tacsimate (pH 5.0) 5% PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.96	58.48

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 143.648	α = 90
b = 154.158	β = 90
c = 87.951	γ = 90

Symmetry
Space Group	P 21 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	RAYONIX MX225HE		2018-07-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 31-ID	0.97931	APS	31-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	CC (Half)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2.02	29.86	99.5	1	11.3	7.5		127544			50.4

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.02	2.13	99.1		0.39	1.1	7.5

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	5TI9	2.02	29.86	121109	6380	99.32	0.1919	0.1893	0.2	0.2428	0.25	RANDOM	50.459

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			-0.14		1.67

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.043
r_dihedral_angle_3_deg	16.958
r_dihedral_angle_4_deg	15.739
r_dihedral_angle_1_deg	5.501
r_angle_refined_deg	1.355
r_angle_other_deg	1.287
r_chiral_restr	0.066
r_gen_planes_refined	0.006
r_bond_refined_d	0.005
r_gen_planes_other	0.003

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.043
r_dihedral_angle_3_deg	16.958
r_dihedral_angle_4_deg	15.739
r_dihedral_angle_1_deg	5.501
r_angle_refined_deg	1.355
r_angle_other_deg	1.287
r_chiral_restr	0.066
r_gen_planes_refined	0.006
r_bond_refined_d	0.005
r_gen_planes_other	0.003
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11593
Nucleic Acid Atoms
Solvent Atoms	1074
Heterogen Atoms	304

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
SCALA	data scaling
PHASER	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.