7OLF

Crystal structure of FMNH2-dependent monooxygenase from Agrobacterium tumefaciens for oxidative desulfurization of sulfoquinovose

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
other		BALBES

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.2 M NaCl, 0.1 M MES pH 6, 26% PEG 6000

Crystal Properties
Matthews coefficient	Solvent content
3.8	67.65

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 203.762	α = 90
b = 203.762	β = 90
c = 110.734	γ = 120

Symmetry
Space Group	P 62 2 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	PIXEL	DECTRIS EIGER2 XE 16M		2018-10-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9763	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	3.4	48.94	99.9	0.119	0.123	0.031	0.998	16	15.8		19137

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.4	3.67	99.9		0.364	0.387	0.127	0.972		8.9

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	BALBES	3.4	48	18114	1002	99.82	0.2206	0.2183	0.2612	RANDOM	75.274

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]
5.06	2.53		5.06		-16.43

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.451
r_dihedral_angle_3_deg	19.219
r_dihedral_angle_4_deg	18.885
r_dihedral_angle_1_deg	8.315
r_angle_refined_deg	1.65
r_angle_other_deg	1.247
r_chiral_restr	0.061
r_bond_refined_d	0.007
r_gen_planes_refined	0.006
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.451
r_dihedral_angle_3_deg	19.219
r_dihedral_angle_4_deg	18.885
r_dihedral_angle_1_deg	8.315
r_angle_refined_deg	1.65
r_angle_other_deg	1.247
r_chiral_restr	0.061
r_bond_refined_d	0.007
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5392
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
xia2	data reduction
BALBES	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 R01GM157729.