7UI3

Apo-form of Human Tryptophan 2,3-Dioxygenase Induced by NADH Binding

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROBATCH	5.6	293	50 mM Sodium Citrate, pH 5.6 2% Tacsimate PEG 3350 (4-12%)

Crystal Properties
Matthews coefficient	Solvent content
2.77	55.55

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 143.855	α = 90
b = 156.264	β = 90
c = 88.986	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 PILATUS 6M	Rh coated flat bent M0, toroidal focusing post-monochromator M1	2021-11-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	1.549750	SSRL	BL9-2

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	3.18	19.974	99.5	0.098	0.106	0.04	1	18.5	12.9		34269

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	3.18	3.34			2.888	3.115	1.163	0.644		13.8

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	6PYZ	3.18	19.974	34173	1774	99.199	0.246	0.2441	0.24	0.2783	0.28	106.154

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]
4.274			-0.966		-3.308

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	25.81
r_dihedral_angle_3_deg	15.577
r_lrange_it	13.605
r_lrange_other	13.605
r_dihedral_angle_4_deg	8.111
r_mcangle_it	7.57
r_mcangle_other	7.57
r_scangle_it	7.336
r_scangle_other	7.335
r_dihedral_angle_1_deg	4.737
r_mcbond_it	4.702
r_mcbond_other	4.702
r_scbond_it	4.457
r_scbond_other	4.455
r_angle_refined_deg	1.276
r_angle_other_deg	1.24
r_nbd_other	0.302
r_nbd_refined	0.242
r_symmetry_nbd_refined	0.195
r_symmetry_nbd_other	0.192
r_nbtor_refined	0.165
r_ncsr_local_group_5	0.136
r_xyhbond_nbd_refined	0.133
r_ncsr_local_group_1	0.129
r_ncsr_local_group_2	0.124
r_ncsr_local_group_3	0.122
r_ncsr_local_group_6	0.119
r_ncsr_local_group_4	0.111
r_symmetry_nbtor_other	0.078
r_chiral_restr	0.05
r_gen_planes_refined	0.005
r_bond_refined_d	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9040
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	64

Software

Software
Software Name	Purpose
REFMAC	refinement
REFMAC	refinement
Coot	model building
Aimless	data scaling
PHASER	phasing
XDS	data reduction