6EZQ | pdb_00006ezq

human Serum Albumin complexed with NBD-C12 fatty acid

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	292	Essentially defatted human serum albumin from Sigma was purified by size exclusion chromatography to obtain pure monomeric protein. The purified HSA was dissolved in 50 mM potassium phosphate, 150 mM sodium chloride (pH 7.5) and concentrated to 2 mM (140 mg/mL). The HSA solution was incubated with a six fold excess of the NBD-labelled fatty acid at 4-5 deg.C for 4 hours. The final concentration of dimethyl sulfoxide was 2% (v/v). The crystal was grown by the hanging drop vapor diffusion method using a reservoir solution containing buffer (2.5 mM potassium phosphate, 7.5 mM sodium chloride, pH 7.0), 0.3% glycerol and polyethylene glycol 3350 (~30%). For crystallization 1 uL of HSA-ligand solution was equilibrated against 1 uL of reservoir solution.

Crystal Properties
Matthews coefficient	Solvent content
2.35	47.57

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 98.48	α = 90
b = 52.72	β = 110.1
c = 123.3	γ = 90

Symmetry
Space Group	C 1 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	DECTRIS PILATUS 6M-F		2017-04-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06DA	0.99992	SLS	X06DA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	2.39	115.79	55.3	0.084	0.084	8.4	3.2		13145			60.21

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.393	2.725	8.5		0.62	0.62	1.6	3.4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION		THROUGHOUT	2.39	115.79	13144	611	55.1	0.187	0.182	0.1884	0.298	0.3114	RANDOM	50.13

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]
1.7181		1.1839	0.9986		-2.7167

RMS Deviations
Key	Refinement Restraint Deviation
t_other_torsion	24.33
t_omega_torsion	2.71
t_angle_deg	1.26
t_bond_d	0.01
t_dihedral_angle_d
t_incorr_chiral_ct
t_pseud_angle
t_trig_c_planes
t_gen_planes
t_it
t_nbd
t_improper_torsion
t_chiral_improper_torsion
t_sum_occupancies
t_utility_distance
t_utility_angle
t_utility_torsion
t_ideal_dist_contact

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4426
Nucleic Acid Atoms
Solvent Atoms	324
Heterogen Atoms	54

Software

Software
Software Name	Purpose
autoPROC	data collection
XDS	data reduction
XDS	data reduction
autoPROC	data scaling
STARANISO	data scaling
BUSTER	refinement
PHASER	phasing