8W1H

Crystal Structure of human Tryptophan 2,3-dioxygenase in complex with PYN3 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
2.72	54.73

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 143.804	α = 90
b = 154.754	β = 90
c = 88.254	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	0.979310	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	2.1	154.75	99.9	0.041	0.049	0.026	0.999	17.4	6.6		115256

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	2.1	2.14			1.528	1.803	0.948	0.477		7

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	2.1	88.41	115171	5857	99.871	0.205	0.2029	0.2339	84.554

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]
-1.706			-1.112		2.818

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	15.04
r_dihedral_angle_3_deg	13.195
r_dihedral_angle_6_deg	12.962
r_lrange_other	11.788
r_lrange_it	11.786
r_scangle_it	7.643
r_scangle_other	7.642
r_mcangle_it	6.338
r_mcangle_other	6.338
r_scbond_it	5.274
r_scbond_other	5.273
r_dihedral_angle_1_deg	4.715
r_mcbond_it	4.483
r_mcbond_other	4.482
r_angle_refined_deg	1.431
r_angle_other_deg	0.514
r_nbd_refined	0.237
r_symmetry_nbd_refined	0.221
r_nbd_other	0.203
r_nbtor_refined	0.188
r_symmetry_nbd_other	0.183
r_xyhbond_nbd_refined	0.136
r_symmetry_xyhbond_nbd_refined	0.134
r_ncsr_local_group_5	0.123
r_ncsr_local_group_6	0.12
r_ncsr_local_group_4	0.115
r_ncsr_local_group_1	0.114
r_ncsr_local_group_3	0.114
r_ncsr_local_group_2	0.113
r_chiral_restr	0.072
r_symmetry_nbtor_other	0.07
r_bond_refined_d	0.007
r_gen_planes_refined	0.007
r_gen_planes_other	0.004
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11618
Nucleic Acid Atoms
Solvent Atoms	113
Heterogen Atoms	332

Software

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