6UBP | pdb_00006ubp

Crystal structure of a photochemical intermediate of human indoleamine 2,3-dioxygenase 1 in complex with carbon monoxide and tryptophan

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROBATCH	10	277	100 mM sodium thiosulfate, 100 mM CAPS, pH 10.0, 20% w/v PEG8000

Crystal Properties
Matthews coefficient	Solvent content
2.9	57.63

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 86.944	α = 90
b = 97.727	β = 90
c = 130.628	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	PIXEL	DECTRIS EIGER X 16M		2019-05-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS-II BEAMLINE 17-ID-2	0.97931	NSLS-II	17-ID-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.95	29.34	99.9	0.098	1	12.2	7.6		24106

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.95	3.13	100		2.015	0.53	1.2	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 (Observed)	R-Work (Depositor)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 5WMU	2.95	29.34	22893	1165	99.85	0.2175	0.2152	0.2641	RANDOM	102.551

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]
-1.87			-3.07		4.94

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.747
r_dihedral_angle_3_deg	18.455
r_dihedral_angle_4_deg	14.062
r_dihedral_angle_1_deg	5.813
r_angle_refined_deg	1.229
r_angle_other_deg	1.034
r_chiral_restr	0.041
r_gen_planes_refined	0.003
r_gen_planes_other	0.003
r_bond_refined_d	0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.747
r_dihedral_angle_3_deg	18.455
r_dihedral_angle_4_deg	14.062
r_dihedral_angle_1_deg	5.813
r_angle_refined_deg	1.229
r_angle_other_deg	1.034
r_chiral_restr	0.041
r_gen_planes_refined	0.003
r_gen_planes_other	0.003
r_bond_refined_d	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5932
Nucleic Acid Atoms
Solvent Atoms	63
Heterogen Atoms	120

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
Aimless	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.