6YG9 | pdb_00006yg9

CRYSTAL STRUCTURE OF HUMAN SERUM ALBUMIN (HSA) IN COMPLEX WITH GN-07.

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
other		in-house structure

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	293	Essentially defatted human serum albumin from Sigma was purified by size exclusion chromatography to obtain pure monomeric protein. The purified HSA was dissolved in 20 mM potassium phosphate (pH 7.0) and concentrated to 120 mg/mL. To the HSA solution we added 10 mM cpdX and 3 mM myristate, dissolved DMSO. The final concentration of DMSO was 5% (v/v). The crystal was grown by the hanging drop vapor diffusion method using a reservoir solution containing 50 mM sodium-potassium-phosphate (pH 7.0), and 30% polyethylene glycol 3350. For crystallization 1 uL of HSA/cpdX solution was equilibrated against 1 uL of reservoir solution. After about one-week, colorless crystals appeared.

Crystal Properties
Matthews coefficient	Solvent content
2.6	52.65

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 197.722	α = 90
b = 38.141	β = 105.88
c = 95.372	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 PILATUS3 X 1M		2016-08-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06DA	1.000000	SLS	X06DA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim I (All)	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	1.89	58.51	96.3	0.077	0.043	0.996	11.7	2.9		53533			31.56

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.89	1.897	91.9		0.62	0.344	0.735	2.1	2.7

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	in-house structure	1.89	58.51	53531	2690	96.2	0.243	0.239	0.258	0.313	0.3443	RANDOM	36.59

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]
-4.477		-4.0171	0.6185		3.8586

RMS Deviations
Key	Refinement Restraint Deviation
t_other_torsion	21.99
t_omega_torsion	2.81
t_angle_deg	1.2
t_bond_d	0.01
t_dihedral_angle_d
t_trig_c_planes
t_gen_planes
t_it
t_nbd
t_improper_torsion
t_pseud_angle
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	4479
Nucleic Acid Atoms
Solvent Atoms	662
Heterogen Atoms	144

Software

Software
Software Name	Purpose
XDS	data reduction
Aimless	data scaling
BUSTER	refinement
PDB_EXTRACT	data extraction
PHASER	phasing