3R1J | pdb_00003r1j

Crystal structure of Alpha-ketoglutarate-dependent taurine dioxygenase from Mycobacterium avium, native form

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1OIJ	PDB ENTRY 1OIJ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	290	Internal tracking number 218640E10. PACT screen condition E10: 0.2 M Na/K Phosphate, 20% PEG3350, MyavA.01188.b.A1 PW28977 at 28.9mg/ml. Cryoprotection: 25% ethylene glycol, VAPOR DIFFUSION, SITTING DROP, temperature 290K

Crystal Properties
Matthews coefficient	Solvent content
2.49	50.73

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 70.95	α = 90
b = 105.31	β = 90
c = 89.25	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	CCD	RIGAKU SATURN 944+		2011-02-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E SUPERBRIGHT	1.541780

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	2.05	41.09	99.7	0.081	15.84	5.7	42701	42570		-3	28.296

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	2.05	2.1	99.3		0.424	3.1	3.4	3124

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MR	THROUGHOUT	PDB ENTRY 1OIJ	2.05	37.78	42570	42393	2139	99.27	0.173	0.173	0.171	0.22	0.2	0.24	RANDOM	25.258

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]
1.04			-0.15		-0.89

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.769
r_dihedral_angle_4_deg	16.796
r_dihedral_angle_3_deg	11.554
r_dihedral_angle_1_deg	6.296
r_scangle_it	3.269
r_scbond_it	2.07
r_angle_refined_deg	1.365
r_mcangle_it	1.252
r_angle_other_deg	0.869
r_mcbond_it	0.702

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.769
r_dihedral_angle_4_deg	16.796
r_dihedral_angle_3_deg	11.554
r_dihedral_angle_1_deg	6.296
r_scangle_it	3.269
r_scbond_it	2.07
r_angle_refined_deg	1.365
r_mcangle_it	1.252
r_angle_other_deg	0.869
r_mcbond_it	0.702
r_mcbond_other	0.195
r_chiral_restr	0.085
r_bond_refined_d	0.013
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3832
Nucleic Acid Atoms
Solvent Atoms	326
Heterogen Atoms	17

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.