3B98

Crystal structure of zebrafish prostacyclin synthase (cytochrome P450 8A1)

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	277	1 microliter of concentrated protein solution (20mg/ml) in gel filtration buffer (20mM Tris-HCl pH 8.0, 150mM NaCl and 5mM beta-mercaptoethanol) was mixed with equal amount of reservoir solution (20% PEG 3350 plus either 50mM Tris-HCl (pH 8.0) or 50mM HEPES (Na-salt; pH 7.5)) and equilibrated against 450 microliter of reservoir solution at 277 K, VAPOR DIFFUSION, HANGING DROP

Crystal Properties
Matthews coefficient	Solvent content
2.24	45.16

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.667	α = 90
b = 87.896	β = 90
c = 190.854	γ = 90

Symmetry
Space Group	P 21 21 21

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	Toroidal FM	2006-12-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSRRC BEAMLINE BL13B1	1.0	NSRRC	BL13B1

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	2.08	30	99.9	0.046	18	5.4	60147	60087	1	1

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)
	2.08	2.15	99.8		0.21	4.3	5.4	5912

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Cut-off Sigma (F)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2IAG	2.08	30	1	1	60147	56980	3031	99.81	0.22921	0.229	0.22735	0.26414	RANDOM	28.442

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]
0.5			-0.06		-0.44

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.333
r_dihedral_angle_4_deg	18.495
r_dihedral_angle_3_deg	15.895
r_dihedral_angle_1_deg	5.289
r_scangle_it	2.48
r_mcangle_it	2.375
r_scbond_it	1.69
r_mcbond_it	1.533
r_angle_refined_deg	1.09
r_nbtor_refined	0.297
r_nbd_refined	0.186
r_symmetry_vdw_refined	0.183
r_symmetry_hbond_refined	0.123
r_xyhbond_nbd_refined	0.116
r_chiral_restr	0.073
r_bond_refined_d	0.008
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7075
Nucleic Acid Atoms
Solvent Atoms	282
Heterogen Atoms	86

Software

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