Experiment: 8UX5

OvsA M401Y/Q430N/A431F from Halomonas utahensis, a hercynine-binding variant with selenoneine-biosynthetic activity

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	8U42

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.6	293	0.1 M sodium acetate pH 4.6, 3.5 M sodium formate, 10 mM sarcosine

Crystal Properties
Matthews coefficient	Solvent content
4.45	72.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 162.174	α = 90
b = 162.174	β = 90
c = 124.663	γ = 120

Symmetry
Space Group	P 65

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 S 16M		2023-05-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CHESS BEAMLINE 7B2	0.9686	CHESS	7B2

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	3.06	29.09	99.84	0.03673	0.05194	0.03673	0.999	14.1	2		35167			106.98

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	3.06	3.169	99.97		0.6614	0.9353	0.6614	0.501	1.09	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	3.06	29.09	1.34	35156	1752	99.96	0.2053	0.2028	0.2028	0.2531	0.2529	94.46

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	17.0437
f_angle_d	1.1029
f_chiral_restr	0.0651
f_plane_restr	0.0217
f_bond_d	0.0077

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7021
Nucleic Acid Atoms
Solvent Atoms	30
Heterogen Atoms	4

Software

Software
Software Name	Purpose
PHENIX	refinement
Coot	model building
XDS	data reduction
XDS	data scaling
PHASER	phasing