8VTQ | pdb_00008vtq

Crystal Structure of human Tryptophan 2,3-dioxygenase in complex with PPN3 inhibitor

X-RAY DIFFRACTION

---

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	54.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 143.818	α = 90
b = 154.732	β = 90
c = 88.407	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		2023-02-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 31-ID	0.979320	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	2.05	154.73	99.6	0.033	0.042	0.026	1	17.4	4.6		123530

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	2.05	2.09			1.493	1.906	1.173	0.428		4.8

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	2.05	105.564	123459	6077	99.512	0.193	0.1914	0.2	0.2176	0.22	79.008

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]
-2.341			-1.53		3.872

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	15.145
r_dihedral_angle_6_deg	13.406
r_dihedral_angle_3_deg	13.32
r_lrange_other	12.519
r_lrange_it	12.516
r_scangle_it	8.843
r_scangle_other	8.843
r_mcangle_it	7.104
r_mcangle_other	7.104
r_scbond_it	6.143
r_scbond_other	6.142
r_mcbond_other	5.059
r_mcbond_it	5.058
r_dihedral_angle_1_deg	4.657
r_angle_refined_deg	1.612
r_angle_other_deg	0.559
r_symmetry_nbd_refined	0.252
r_nbd_other	0.248
r_nbd_refined	0.236
r_nbtor_refined	0.189
r_symmetry_nbd_other	0.182
r_xyhbond_nbd_refined	0.141
r_symmetry_xyhbond_nbd_refined	0.125
r_ncsr_local_group_6	0.124
r_ncsr_local_group_4	0.119
r_ncsr_local_group_5	0.115
r_ncsr_local_group_3	0.114
r_ncsr_local_group_2	0.113
r_ncsr_local_group_1	0.108
r_chiral_restr	0.078
r_symmetry_nbtor_other	0.071
r_symmetry_xyhbond_nbd_other	0.037
r_bond_refined_d	0.009
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	11724
Nucleic Acid Atoms
Solvent Atoms	146
Heterogen Atoms	336

Software

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