9PV1 | pdb_00009pv1

Biotin halogenase BtnX, anaerobic structure with Fe(II), biotin, alpha-ketoglutarate, chloride

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold	A8LT50	The A8LT50 homodimer was used as the search model

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	298	1:1 v/v mixing of crystallographic solution (26% w/v PEG4000, 0.1 M TRIS, pH 8.0, 0.2 M lithium sulfate) with protein solution (10 mg/mL purified BtnX, 1.0 mM alpha-ketoglutarate, 1.75 mM biotin, 50 mM NaCl). After crystallization 0.5 M of (NH4)2Fe(SO4)2 was added, followed by 30% v/v ethylene glycol

Crystal Properties
Matthews coefficient	Solvent content
2.52	51.28

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.868	α = 90
b = 82.775	β = 90
c = 173.355	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 PILATUS3 S 6M		2025-05-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.3.1	1.11	ALS	8.3.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.2	86.68	97.6	0.07014	0.02075	0.999	16.89	11.7		222979			13.69

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.2	1.243			0.9933	0.4138	0.722	1.66

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	1.2	86.68	1.35	222904	11191	97.52	0.148	0.1469	0.147	0.1696	0.1697	21.15

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	13.2995
f_angle_d	1.0727
f_chiral_restr	0.0851
f_plane_restr	0.0126
f_bond_d	0.0077

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5018
Nucleic Acid Atoms
Solvent Atoms	731
Heterogen Atoms	123

Software

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