9WNX | pdb_00009wnx

beta-lactoglobulin in complex with Perfluorooctanesulfonic acid (PFOS)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION		293.15	1.8 M sodium phosphate monobasic monohydrate and potassium phosphate dibasic at pH 8.2

Crystal Properties
Matthews coefficient	Solvent content
2.477	50.38

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.36	α = 90
b = 53.36	β = 90
c = 110.197	γ = 120

Symmetry
Space Group	P 32 2 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	RIGAKU HyPix-6000HE		2025-01-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.54184

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.5	28.75	99.9	0.159	14.6	18.83		6720

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	2.5	2.6	100		0.538	1.5	13.84

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	AlphaFold	2.5	23.116	6690	343	99.776	0.198	0.1946	0.1972	0.2613	0.2653	66.611

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]
-0.177	-0.089		-0.177		0.575

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	19.648
r_lrange_it	16.334
r_dihedral_angle_6_deg	13.343
r_scangle_it	11.879
r_mcangle_it	9.15
r_dihedral_angle_1_deg	8.196
r_scbond_it	7.952
r_dihedral_angle_2_deg	7.288
r_mcbond_it	5.888
r_angle_refined_deg	2.107
r_nbtor_refined	0.305
r_symmetry_nbd_refined	0.279
r_nbd_refined	0.255
r_xyhbond_nbd_refined	0.197
r_chiral_restr	0.146
r_symmetry_xyhbond_nbd_refined	0.113
r_gen_planes_refined	0.009
r_bond_refined_d	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1258
Nucleic Acid Atoms
Solvent Atoms	9
Heterogen Atoms	30

Software

Software
Software Name	Purpose
REFMAC	refinement
CrysalisPro	data reduction
CrysalisPro	data scaling
MOLREP	phasing