9B1Q

Crystal Structure of human Tryptophan 2,3-dioxygenase in complex with PYN1 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
2.69	54.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 142.959	α = 90
b = 154.17	β = 90
c = 88.277	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 EIGER X 16M		2024-02-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS-II BEAMLINE 17-ID-2	0.97934	NSLS-II	17-ID-2

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	2.624	34.291	93.7	0.1357	0.148	0.0582	0.998	9.62	6.38		31809

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)
	2.624	2.997	77.1		1.0604	1.1417	0.42	0.647	1.79	7.31	1590

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	2.624	34.291	31808	1625	53.781	0.205	0.2023	0.2583	75.541

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]
1.094			-0.289		-0.805

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	18.277
r_dihedral_angle_3_deg	14.554
r_lrange_it	11.897
r_lrange_other	11.897
r_dihedral_angle_6_deg	10.713
r_scangle_it	6.086
r_scangle_other	6.085
r_mcangle_other	5.642
r_mcangle_it	5.641
r_dihedral_angle_1_deg	4.747
r_scbond_it	3.628
r_scbond_other	3.624
r_mcbond_it	3.37
r_mcbond_other	3.365
r_angle_refined_deg	1.417
r_angle_other_deg	0.481
r_nbd_refined	0.241
r_symmetry_nbd_other	0.204
r_nbd_other	0.201
r_nbtor_refined	0.198
r_symmetry_nbd_refined	0.159
r_xyhbond_nbd_refined	0.149
r_symmetry_xyhbond_nbd_refined	0.148
r_ncsr_local_group_6	0.123
r_ncsr_local_group_4	0.121
r_ncsr_local_group_2	0.12
r_ncsr_local_group_5	0.12
r_ncsr_local_group_3	0.115
r_ncsr_local_group_1	0.112
r_symmetry_xyhbond_nbd_other	0.092
r_symmetry_nbtor_other	0.077
r_chiral_restr	0.06
r_bond_refined_d	0.007
r_gen_planes_refined	0.006
r_gen_planes_other	0.003
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11596
Nucleic Acid Atoms
Solvent Atoms	12
Heterogen Atoms	332

Software

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