X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2IAGPDB ENTRY 2IAG

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8277Crystallization of native human prostacyclin synthase (hPGIS). The native recombinant PGIS (25 mg/ml in the gel filtration 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 microliter of diluted seeds was added into a 10 microliter drop of freshly concentrated PGIS sample, and equilibrated at 4 C against 450 microliter of the gel filtration buffer. Crystallization of hPGIS-minoxidil complex: The inhibitor-enzyme complex was prepared by adding minoxidil (final concentration 0.1 mM) to a 20 mg/ml hPGIS stock solution. Crystals of the complex were then obtained by co-crystallization, with the technique described above using ligand-free hPGIS microcrystals as seeds., VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.3547.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.762α = 90
b = 106.072β = 91.81
c = 73.901γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102006-09-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSRRC BEAMLINE BL13C10.97622NSRRCBL13C1

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
11.623099.50.0416.13.713431913364811
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)
1.621.6697.50.3232

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 2IAG1.6229.0911133648126835677099.560.2090.204120.202840.22805RANDOM21.337
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
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.743
r_dihedral_angle_4_deg14.624
r_dihedral_angle_3_deg14.306
r_dihedral_angle_1_deg5.12
r_scangle_it2.201
r_scbond_it1.434
r_angle_refined_deg1.046
r_mcangle_it1.012
r_mcbond_it0.599
r_nbtor_refined0.304
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.743
r_dihedral_angle_4_deg14.624
r_dihedral_angle_3_deg14.306
r_dihedral_angle_1_deg5.12
r_scangle_it2.201
r_scbond_it1.434
r_angle_refined_deg1.046
r_mcangle_it1.012
r_mcbond_it0.599
r_nbtor_refined0.304
r_nbd_refined0.193
r_symmetry_vdw_refined0.152
r_symmetry_hbond_refined0.108
r_xyhbond_nbd_refined0.102
r_chiral_restr0.07
r_bond_refined_d0.007
r_gen_planes_refined0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7631
Nucleic Acid Atoms
Solvent Atoms765
Heterogen Atoms156

Software

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