2IAG

Crystal structure of human prostacyclin synthase

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	277	The native recombinant PGIS (25 mg/ml in the buffer containing 20 mM Tris, pH 8.0 and 150 mM NaCl) was found to crystallize spontaneously into needle clusters in the Eppendorf tube when stored at 4 C for about a week. A combination of microseeding technique and the hanging-drop vapor-diffusion method was then used to improve crystal quality. Specifically, seed stock was prepared by crushing these initial PGIS needle clusters with the Seed Bead Kit (Hampton Research). Following four 10-fold serial dilutions of the seed stock using the gel filtration buffer, 1 micro-l of diluted seeds was added into a 10 micro-l drop of freshly concentrated PGIS sample, and equilibrated at 4 C against 450 micro-l of the gel filtration buffer. High quality single crystals of PGIS were most often obtained using 100- or 1000-fold diluted seed stock, and reached suitable size (~ 0.05,0.05 ~ 0.1 mm3) within one week., VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.39	48.45

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 67.733	α = 90
b = 105.596	β = 92.01
c = 73.95	γ = 90

Symmetry
Space Group	P 1 21 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	CCD	ADSC QUANTUM 315		2006-06-29	M	SINGLE WAVELENGTH
2	1	x-ray	100	CCD	ADSC QUANTUM 4		2006-05-15	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSRRC BEAMLINE BL13B1	0.980127	NSRRC	BL13B1
2	SYNCHROTRON	SPRING-8 BEAMLINE BL12B2	0.9537, 0.9793	SPring-8	BL12B2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.15	30	90.9	0.063	12.7	2.8	56459	51322

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.15	2.23	93.5		0.35	3.1

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	2.15	20.15	48702	2601	90.96	0.20407	0.2009	0.26313	RANDOM	26.948

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.256
r_dihedral_angle_4_deg	18.433
r_dihedral_angle_3_deg	17.588
r_dihedral_angle_1_deg	6.177
r_scangle_it	2.987
r_scbond_it	1.961
r_angle_refined_deg	1.38
r_mcangle_it	1.213
r_mcbond_it	0.642
r_nbtor_refined	0.304
r_nbd_refined	0.205
r_symmetry_vdw_refined	0.192
r_xyhbond_nbd_refined	0.16
r_symmetry_hbond_refined	0.154
r_chiral_restr	0.095
r_bond_refined_d	0.011
r_gen_planes_refined	0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7611
Nucleic Acid Atoms
Solvent Atoms	435
Heterogen Atoms	87

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SOLVE	phasing