9AT2

Crystal Structure of human Tryptophan 2,3-dioxygenase in complex with PAN3 inhibitor

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6PYZ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROBATCH		298	50 mM Sodium Citrate pH 5.6, 2.0% Tacsimate pH 5.0, 5.0% PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.74	55.04

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 144.042	α = 90
b = 155.112	β = 90
c = 88.515	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	PIXEL	DECTRIS PILATUS3 S 6M		2023-03-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 31-ID	0.979300	APS	31-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	2.25	155.11	99.9	0.058	0.069	0.037	0.999	12.7	6.5		94512

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.25	2.29			1.451	1.741	0.946	0.47		6.2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.25	88.672	94450	4874	99.781	0.203	0.2015	0.2233	88.555

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]
-1.138			0.045		1.093

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	15.353
r_dihedral_angle_3_deg	13.941
r_dihedral_angle_6_deg	13.932
r_lrange_it	13.025
r_lrange_other	13.025
r_scangle_it	8.937
r_scangle_other	8.937
r_mcangle_it	7.217
r_mcangle_other	7.216
r_scbond_it	6.051
r_scbond_other	6.051
r_mcbond_it	4.997
r_mcbond_other	4.992
r_dihedral_angle_1_deg	4.636
r_angle_refined_deg	1.529
r_angle_other_deg	0.537
r_symmetry_xyhbond_nbd_refined	0.276
r_symmetry_nbd_refined	0.263
r_nbd_other	0.254
r_nbd_refined	0.234
r_nbtor_refined	0.187
r_symmetry_nbd_other	0.183
r_xyhbond_nbd_refined	0.146
r_ncsr_local_group_6	0.126
r_ncsr_local_group_2	0.12
r_ncsr_local_group_4	0.116
r_ncsr_local_group_5	0.116
r_ncsr_local_group_1	0.112
r_ncsr_local_group_3	0.11
r_chiral_restr	0.072
r_symmetry_nbtor_other	0.07
r_symmetry_xyhbond_nbd_other	0.07
r_bond_refined_d	0.008
r_gen_planes_refined	0.008
r_gen_planes_other	0.004
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11644
Nucleic Acid Atoms
Solvent Atoms	23
Heterogen Atoms	340

Software

Software
Software Name	Purpose
REFMAC	refinement
autoPROC	data reduction
Aimless	data scaling
PHASER	phasing