6PZ1

Crystal Structure of human Indoleamine 2,3-Dioxygenase 1 in complex with PF-06840003 in Active Site and Si site

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5WMU

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROBATCH	10	277	100 mM Sodium thiosulfate, 100 mM CAPS buffer pH 10.0, and 20% (w/v) PEG 8000

Crystal Properties
Matthews coefficient	Solvent content
2.95	58.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 87.479	α = 90
b = 97.858	β = 90
c = 131.966	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	RAYONIX MX225HE		2018-02-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 31-ID	0.97931	APS	31-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	2.65	78.61	99.8	0.99	7.4	7.1		33561

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.65	2.79	100		0.54	1

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	5WMU	2.65	40	31777	1671	99.61	0.2225	0.2201	0.2698	RANDOM	83.542

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]
-1.76			-3.47		5.23

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.511
r_dihedral_angle_3_deg	18.762
r_dihedral_angle_4_deg	18.19
r_dihedral_angle_1_deg	6.477
r_angle_refined_deg	1.416
r_angle_other_deg	1.088
r_chiral_restr	0.052
r_gen_planes_refined	0.004
r_bond_refined_d	0.003
r_gen_planes_other	0.003

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.511
r_dihedral_angle_3_deg	18.762
r_dihedral_angle_4_deg	18.19
r_dihedral_angle_1_deg	6.477
r_angle_refined_deg	1.416
r_angle_other_deg	1.088
r_chiral_restr	0.052
r_gen_planes_refined	0.004
r_bond_refined_d	0.003
r_gen_planes_other	0.003
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5963
Nucleic Acid Atoms
Solvent Atoms	188
Heterogen Atoms	167

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
SCALA	data scaling
PHASER	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.