4J5I

Crystal structure of an alpha-ketoglutarate-dependent taurine dioxygenase from Mycobacterium smegmatis

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3R1J	PDB entry 3R1J

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	289	MysmA.01188.a.A1 PS00650 at 20 mg/mL against Morpheus condition A2, 10% PEG 8000, 20% ethylene glycol, 30 mM MgCl, 30 mM CaCl2, 0.1 M MES/imidazole pH 6.5, crystal tracking ID 233128a2, unique puck ID oqa0-7, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.38	48.42

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 77.01	α = 90
b = 166.68	β = 90.57
c = 99.72	γ = 90

Symmetry
Space Group	P 1 21 1

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	RIGAKU SATURN 944+	VariMax	2012-09-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E+ SUPERBRIGHT	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.6	50	99	0.113	10.33	3.5	77167	76380		-3	30.271

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.6	2.67	99.1		0.393	3.68

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	PDB entry 3R1J	2.6	49.4	76379	3833	98.98	0.2122	0.211	0.2345	RANDOM	26.9535

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]
1.52		0.52	-1.83		0.3

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.11
r_dihedral_angle_3_deg	14.654
r_dihedral_angle_4_deg	13.366
r_dihedral_angle_1_deg	6.06
r_mcangle_it	1.643
r_angle_refined_deg	1.251
r_angle_other_deg	1.095
r_mcbond_it	0.971
r_mcbond_other	0.971
r_chiral_restr	0.069

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.11
r_dihedral_angle_3_deg	14.654
r_dihedral_angle_4_deg	13.366
r_dihedral_angle_1_deg	6.06
r_mcangle_it	1.643
r_angle_refined_deg	1.251
r_angle_other_deg	1.095
r_mcbond_it	0.971
r_mcbond_other	0.971
r_chiral_restr	0.069
r_bond_refined_d	0.009
r_bond_other_d	0.006
r_gen_planes_refined	0.006
r_gen_planes_other	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	15795
Nucleic Acid Atoms
Solvent Atoms	509
Heterogen Atoms	13

Software

Software
Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
StructureStudio	data collection
XDS	data reduction

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.