8UX5 | pdb_00008ux5

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	0.2	0.2531	0.25	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

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.