9WNV | pdb_00009wnv

beta-lactoglobulin in complex with perfluorooctanoic acid (PFOA)

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	8.2	293.15	1.8 M sodium phosphate monobasic monohydrate and potassium phosphate dibasic at pH 8.2

Crystal Properties
Matthews coefficient	Solvent content
2.4515	49.858

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.133	α = 90
b = 53.133	β = 90
c = 109.983	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		2025-01-03	M	SINGLE WAVELENGTH

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

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	28.67	99.9	1	23.5	14.66		12737

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	2.05			0.935	4.5

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	22.53	12681	616	99.748	0.209	0.2067	0.2066	0.2518	0.252	42.365

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]
-0.066	-0.033		-0.066		0.215

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	16.818
r_dihedral_angle_6_deg	14.127
r_dihedral_angle_2_deg	10.3
r_lrange_it	9.91
r_dihedral_angle_1_deg	8.028
r_scangle_it	6.75
r_mcangle_it	4.963
r_scbond_it	4.373
r_mcbond_it	3.103
r_angle_refined_deg	2.045
r_nbtor_refined	0.317
r_symmetry_nbd_refined	0.287
r_nbd_refined	0.264
r_xyhbond_nbd_refined	0.247
r_symmetry_xyhbond_nbd_refined	0.204
r_metal_ion_refined	0.202
r_chiral_restr	0.134
r_gen_planes_refined	0.009
r_bond_refined_d	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1257
Nucleic Acid Atoms
Solvent Atoms	49
Heterogen Atoms	41

Software

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