3EBY

Crystal structure of the beta subunit of a putative aromatic-ring-hydroxylating dioxygenase (YP_001165631.1) from NOVOSPHINGOBIUM AROMATICIVORANS DSM 12444 at 1.75 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.9	277	0.2000M KCl, 20.0000% PEG-3350, No Buffer pH 6.9, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.48	50.46

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 80.29	α = 90
b = 80.29	β = 90
c = 145.02	γ = 120

Symmetry
Space Group	H 3 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	MARMOSAIC 325 mm CCD	Flat collimating mirror, toroid focusing mirror	2008-08-10	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.91837,0.97929,0.97915	SSRL	BL9-2

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	1.75	26.764	99.2	0.06	12.89	5.5		18394		-3	21.006

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	1.75	1.81	97.1		0.577	1.9

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	MAD	THROUGHOUT	1.75	26.764	18393	939	99.82	0.17	0.168	0.205	RANDOM	23.605

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]
-0.67	-0.33		-0.67		1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.152
r_dihedral_angle_4_deg	16.352
r_dihedral_angle_3_deg	11.182
r_dihedral_angle_1_deg	5.994
r_scangle_it	5.655
r_scbond_it	4.283
r_mcangle_it	3.462
r_mcbond_it	2.733
r_angle_refined_deg	1.046
r_angle_other_deg	0.697
r_mcbond_other	0.687
r_symmetry_vdw_other	0.276
r_nbd_other	0.218
r_nbd_refined	0.214
r_xyhbond_nbd_refined	0.201
r_symmetry_hbond_refined	0.201
r_nbtor_refined	0.174
r_symmetry_vdw_refined	0.104
r_chiral_restr	0.086
r_nbtor_other	0.084
r_bond_refined_d	0.018
r_gen_planes_refined	0.011
r_bond_other_d	0.004
r_gen_planes_other	0.002
r_symmetry_hbond_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1170
Nucleic Acid Atoms
Solvent Atoms	173
Heterogen Atoms	1

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
SHELXD	phasing
autoSHARP	phasing