3B99

Crystal structure of zebrafish prostacyclin synthase (cytochrome P450 8A1) in complex with substrate analog U51605

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2IAG	PDB ENTRY 2IAG

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	Soaking	7.5	277	The crystal of prostacyclin synthase-U51605 complex was prepared by soaking the ligand-free crystals in 2 microliter of substitute mother liquor (23% PEG 3350, 50mM HEPES (Na-salt; pH 7.5)) containing 0.25mM of U51605 for a week, Soaking, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.23	44.86

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.47	α = 90
b = 88.044	β = 90
c = 190.142	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	2007-04-07	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	2.5	30	92.3	0.064	12.9	4.7	35343	32622	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)
1	2.5	2.59	94.2		0.302	2.8	4.4	3269

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	2.5	27.75	1	1	35343	30957	1643	91.58	0.21817	0.218	0.21414	0.29209	RANDOM	32.075

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]
-0.39			-0.44		0.83

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.455
r_dihedral_angle_3_deg	18.059
r_dihedral_angle_4_deg	18.031
r_dihedral_angle_1_deg	5.472
r_mcangle_it	2.913
r_scangle_it	2.754
r_scbond_it	1.895
r_mcbond_it	1.856
r_angle_refined_deg	1.404
r_nbtor_refined	0.306

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.455
r_dihedral_angle_3_deg	18.059
r_dihedral_angle_4_deg	18.031
r_dihedral_angle_1_deg	5.472
r_mcangle_it	2.913
r_scangle_it	2.754
r_scbond_it	1.895
r_mcbond_it	1.856
r_angle_refined_deg	1.404
r_nbtor_refined	0.306
r_nbd_refined	0.206
r_symmetry_hbond_refined	0.196
r_xyhbond_nbd_refined	0.153
r_symmetry_vdw_refined	0.153
r_chiral_restr	0.09
r_bond_refined_d	0.009
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6991
Nucleic Acid Atoms
Solvent Atoms	223
Heterogen Atoms	230

Software

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.