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)
TypeSourceAccession CodeDetails
experimental modelPDB 2IAGPDB ENTRY 2IAG

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1Soaking7.5277The 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 coefficientSolvent content
2.2344.86

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.47α = 90
b = 88.044β = 90
c = 190.142γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315Toroidal FM2007-04-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSRRC BEAMLINE BL13B11.0NSRRCBL13B1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.53092.30.06412.94.7353433262211
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.52.5994.20.3022.84.43269

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2IAG2.527.75113534330957164391.580.218170.2180.214140.29209RANDOM32.075
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]
-0.39-0.440.83
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.455
r_dihedral_angle_3_deg18.059
r_dihedral_angle_4_deg18.031
r_dihedral_angle_1_deg5.472
r_mcangle_it2.913
r_scangle_it2.754
r_scbond_it1.895
r_mcbond_it1.856
r_angle_refined_deg1.404
r_nbtor_refined0.306
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.455
r_dihedral_angle_3_deg18.059
r_dihedral_angle_4_deg18.031
r_dihedral_angle_1_deg5.472
r_mcangle_it2.913
r_scangle_it2.754
r_scbond_it1.895
r_mcbond_it1.856
r_angle_refined_deg1.404
r_nbtor_refined0.306
r_nbd_refined0.206
r_symmetry_hbond_refined0.196
r_xyhbond_nbd_refined0.153
r_symmetry_vdw_refined0.153
r_chiral_restr0.09
r_bond_refined_d0.009
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6991
Nucleic Acid Atoms
Solvent Atoms223
Heterogen Atoms230

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing