3FO7

Simultaneous inhibition of anti-coagulation and inflammation: Crystal structure of phospholipase A2 complexed with indomethacin at 1.4 A resolution reveals the presence of the new common ligand binding site


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1SKG 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP72980.3M AMMONIUM SULPHATE, 30% PEG 4000, pH 7.00, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.448.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.66α = 90
b = 51.66β = 90
c = 48.003γ = 90
Symmetry
Space GroupP 43

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray298IMAGE PLATEMARRESEARCHMirror2006-10-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU3001.5414

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
11.451.9999.20.04519.519.7249392493921.5
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)
1.41.421000.4182.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)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 REPLACEMENTTHROUGHOUT1SKG1.451.992493923491126299.20.190420.1880.1880.202RANDOM22.37
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]
0.340.34-0.68
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg16.907
r_dihedral_angle_1_deg2.317
r_scangle_it2.081
r_angle_refined_deg1.675
r_scbond_it1.304
r_mcangle_it1.116
r_angle_other_deg0.755
r_mcbond_it0.604
r_nbd_refined0.395
r_nbd_other0.232
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg16.907
r_dihedral_angle_1_deg2.317
r_scangle_it2.081
r_angle_refined_deg1.675
r_scbond_it1.304
r_mcangle_it1.116
r_angle_other_deg0.755
r_mcbond_it0.604
r_nbd_refined0.395
r_nbd_other0.232
r_symmetry_vdw_other0.207
r_symmetry_hbond_refined0.204
r_xyhbond_nbd_refined0.189
r_symmetry_vdw_refined0.124
r_xyhbond_nbd_other0.083
r_chiral_restr0.08
r_symmetry_hbond_other0.008
r_bond_refined_d0.007
r_gen_planes_refined0.005
r_gen_planes_other0.002
r_bond_other_d0.001
r_dihedral_angle_2_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_nbtor_other
r_metal_ion_refined
r_metal_ion_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 AtomsNumber
Protein Atoms998
Nucleic Acid Atoms
Solvent Atoms224
Heterogen Atoms45

Software

Software
Software NamePurpose
HKL-2000data collection
AMoREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling