5M4O

Crystal structure of hydroquinone 1,2-dioxygenase from Sphingomonas sp. TTNP3 in complex with 4-nitrophenol

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	6.5	296	14% PEG 3350, 0.35 M MgCl2 and 0.1 M Mes

Crystal Properties
Matthews coefficient	Solvent content
2.2	44.06

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 88.992	α = 90
b = 125.982	β = 105.14
c = 92.331	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	MARMOSAIC 225 mm CCD		2016-05-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-2	0.8729	ESRF	ID23-2

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	2.1	29.7	98.3	0.161	0.99	6.54	4.04		112445		-3	33.313

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	2.1	2.23	94.7		0.883	0.636	1.56

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	FOURIER SYNTHESIS	THROUGHOUT	2.1	29.697	106980	5436	98.31	0.191	0.1881	0.2486	RANDOM	33.931

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]
-3.26		0.61	-1.86		4.18

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.659
r_dihedral_angle_4_deg	17.588
r_dihedral_angle_3_deg	14.899
r_dihedral_angle_1_deg	6.257
r_mcangle_it	2.099
r_scbond_it	1.703
r_mcbond_it	1.289
r_angle_refined_deg	1.18
r_chiral_restr	0.082
r_bond_refined_d	0.007

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.659
r_dihedral_angle_4_deg	17.588
r_dihedral_angle_3_deg	14.899
r_dihedral_angle_1_deg	6.257
r_mcangle_it	2.099
r_scbond_it	1.703
r_mcbond_it	1.289
r_angle_refined_deg	1.18
r_chiral_restr	0.082
r_bond_refined_d	0.007
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	15329
Nucleic Acid Atoms
Solvent Atoms	1076
Heterogen Atoms	44

Software

Software
Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XSCALE	data reduction
REFMAC	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 R01GM133198.