Experiment: 7YJ0

Structural basis of oxepinone formation by a flavin-monooxygenase VibO

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		289	0.2 M Ammonium acetate, 0.1 M Tris pH 8.0, 16% w/v Polyethylene glycol 10,000

Crystal Properties
Matthews coefficient	Solvent content
2.43	49.29

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 77.083	α = 89.874
b = 92.504	β = 74.919
c = 104.639	γ = 75.746

Symmetry
Space Group	P 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	PIXEL	DECTRIS PILATUS3 S 2M		2021-11-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL17B1	0.97915	SSRF	BL17B1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.425	71.979	92.8	0.995	6	3.5		94891			42.67

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.425	2.467			0.814	2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.43	34.38	2	94834	4737	92.75	0.1789	0.1762	0.1779	0.2297	0.2288	51.12

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	16.133
f_angle_d	1.1475
f_chiral_restr	0.0681
f_bond_d	0.0104
f_plane_restr	0.0071

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	19255
Nucleic Acid Atoms
Solvent Atoms	444
Heterogen Atoms	218

Software

Software
Software Name	Purpose
PHENIX	refinement
autoPROC	data scaling
PDB_EXTRACT	data extraction
autoPROC	data reduction
PHENIX	phasing