9B17 | pdb_00009b17

Crystal Structure of human Tryptophan 2,3-dioxygenase in complex with PAN1 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
2.71	54.61

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 143.61	α = 90
b = 154.014	β = 90
c = 88.58	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	2.648	34.29	92.7	0.1074	0.1207	0.0541	0.998	10.89	4.83		36145

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)
	2.648	3.006	62.2		0.8788	0.9814	0.4322	0.611	1.84	5.1	1808

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.65	34.29	36137	1788	62.493	0.192	0.1899	0.19	0.2344	0.23	72.776

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]
1.588			-0.576		-1.013

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	21.05
r_dihedral_angle_3_deg	14.342
r_dihedral_angle_6_deg	11.473
r_lrange_it	10.514
r_lrange_other	10.514
r_scangle_it	5.797
r_scangle_other	5.797
r_mcangle_it	5.161
r_mcangle_other	5.16
r_dihedral_angle_1_deg	4.962
r_scbond_it	3.415
r_scbond_other	3.414
r_mcbond_it	3.088
r_mcbond_other	3.081
r_angle_refined_deg	1.402
r_angle_other_deg	0.489
r_nbd_refined	0.242
r_nbd_other	0.197
r_nbtor_refined	0.196
r_symmetry_nbd_other	0.193
r_symmetry_nbd_refined	0.155
r_xyhbond_nbd_refined	0.149
r_ncsr_local_group_4	0.119
r_ncsr_local_group_5	0.118
r_ncsr_local_group_6	0.117
r_ncsr_local_group_2	0.114
r_ncsr_local_group_3	0.113
r_ncsr_local_group_1	0.109
r_symmetry_xyhbond_nbd_refined	0.093
r_symmetry_nbtor_other	0.074
r_chiral_restr	0.063
r_bond_refined_d	0.006
r_gen_planes_refined	0.006
r_gen_planes_other	0.004
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11616
Nucleic Acid Atoms
Solvent Atoms	19
Heterogen Atoms	340

Software

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