3VB0

Crystal structure of 2,2',3-trihydroxybiphenyl 1,2-dioxygenase from dibenzofuran-degrading Sphingomonas wittichii strain RW1

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	294	1.4-2.0 M (NH4)2SO4, 2% PEG 400 and 0.1 M PIPES at pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
1.727	28.79

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 131.587	α = 90
b = 131.587	β = 90
c = 103.146	γ = 90

Symmetry
Space Group	P 43 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	IMAGE PLATE	MAR scanner 300 mm plate		2005-07-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	1.0	APS	22-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	2.1	92.85	98.1	0.094	0.094	14.6	7.4	53614	51572		-3	36

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.1	2.18	91.1		0.499	0.499	2	3	4815

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	Crystal structure of 2,3-dihydroxybiphenyl 1,2-dioxygenase from Rhodococcus globerulus strain P6	2.1	92.85	52592	49806	2647	97.94	0.25559	0.25559	0.25378	0.28906	RANDOM	23.474

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]
-0.27			-0.27		0.54

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.983
r_dihedral_angle_4_deg	16.161
r_dihedral_angle_3_deg	13.838
r_dihedral_angle_1_deg	5.562
r_scangle_it	2.034
r_scbond_it	1.284
r_angle_refined_deg	1.064
r_mcangle_it	0.966
r_mcbond_it	0.565
r_nbtor_refined	0.3

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.983
r_dihedral_angle_4_deg	16.161
r_dihedral_angle_3_deg	13.838
r_dihedral_angle_1_deg	5.562
r_scangle_it	2.034
r_scbond_it	1.284
r_angle_refined_deg	1.064
r_mcangle_it	0.966
r_mcbond_it	0.565
r_nbtor_refined	0.3
r_symmetry_vdw_refined	0.246
r_nbd_refined	0.206
r_symmetry_hbond_refined	0.145
r_xyhbond_nbd_refined	0.126
r_chiral_restr	0.078
r_bond_refined_d	0.009
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8952
Nucleic Acid Atoms
Solvent Atoms	158
Heterogen Atoms	52

Software

Software
Software Name	Purpose
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

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 R01GM133198.