9WNW | pdb_00009wnw

beta-lactoglobulin in complex with Perfluorodecanoic acid (PFDA)

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
2.46746182	50.1821747

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.023	α = 90
b = 53.023	β = 90
c = 111.157	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		2024-12-13	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)	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	28.84	100	1	23.9	14.39		12824

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	100		0.903	4.1	10.95

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	22.495	12781	638	99.844	0.191	0.1886	0.1888	0.2384	0.2384	38.765

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]
0.024	0.012		0.024		-0.077

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	16.334
r_dihedral_angle_6_deg	13.973
r_dihedral_angle_2_deg	10.393
r_lrange_it	9.835
r_dihedral_angle_1_deg	6.93
r_scangle_it	6.698
r_scbond_it	4.463
r_mcangle_it	3.858
r_mcbond_it	2.613
r_angle_refined_deg	1.974
r_nbtor_refined	0.314
r_xyhbond_nbd_refined	0.289
r_symmetry_nbd_refined	0.289
r_nbd_refined	0.269
r_symmetry_xyhbond_nbd_refined	0.198
r_chiral_restr	0.134
r_metal_ion_refined	0.024
r_bond_refined_d	0.008
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1249
Nucleic Acid Atoms
Solvent Atoms	26
Heterogen Atoms	50

Software

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