7OH2

Crystal structure of FMNH2-dependent monooxygenase for oxidative desulfurization of sulfoquinovose

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7OLF	D_1292115543

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.2 M NaNO3, 20% PEG 3350k, protein to mother liquor ratio 1:2

Crystal Properties
Matthews coefficient	Solvent content
2.13	42.13

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 71.164	α = 90
b = 100.401	β = 90
c = 104.653	γ = 90

Symmetry
Space Group	P 21 21 21

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 PILATUS 6M-F		2020-02-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.9119	Diamond	I04-1

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	1.9	72.45	100	0.168	0.175	0.048	0.998	12.7	13.4		59830

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	1.9	1.94	100		1.77	1.84	0.498	0.877		13.8

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	D_1292115543	1.9	71.01	56981	2773	99.99	0.1686	0.1673	0.1961	RANDOM	23.722

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]
-1.49			-0.96		2.45

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.096
r_dihedral_angle_4_deg	17.273
r_dihedral_angle_3_deg	12.596
r_dihedral_angle_1_deg	6.552
r_angle_refined_deg	1.579
r_angle_other_deg	1.472
r_chiral_restr	0.084
r_bond_refined_d	0.011
r_gen_planes_refined	0.009
r_bond_other_d	0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.096
r_dihedral_angle_4_deg	17.273
r_dihedral_angle_3_deg	12.596
r_dihedral_angle_1_deg	6.552
r_angle_refined_deg	1.579
r_angle_other_deg	1.472
r_chiral_restr	0.084
r_bond_refined_d	0.011
r_gen_planes_refined	0.009
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5550
Nucleic Acid Atoms
Solvent Atoms	491
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.