3H1X

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 1FB2PDB ENTRY 1FB2

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP72980.3M AMMONIUM SULPHATE, 30% PEG 4000 , pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.3547.65

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
11.451.9999.20.04519.519.72493924939
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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1FB21.451.99249392423551899.250.190420.190130.20661RANDOM21.888
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]
0.360.36-0.73
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg18.803
r_dihedral_angle_1_deg4.7
r_scangle_it3.152
r_angle_refined_deg2.273
r_sphericity_free2.081
r_scbond_it2.066
r_sphericity_bonded1.968
r_mcangle_it1.821
r_rigid_bond_restr1.252
r_mcbond_it1.114
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg18.803
r_dihedral_angle_1_deg4.7
r_scangle_it3.152
r_angle_refined_deg2.273
r_sphericity_free2.081
r_scbond_it2.066
r_sphericity_bonded1.968
r_mcangle_it1.821
r_rigid_bond_restr1.252
r_mcbond_it1.114
r_angle_other_deg1.014
r_nbd_refined0.406
r_nbd_other0.249
r_symmetry_vdw_other0.242
r_xyhbond_nbd_refined0.189
r_symmetry_hbond_refined0.154
r_symmetry_vdw_refined0.15
r_chiral_restr0.107
r_xyhbond_nbd_other0.028
r_bond_refined_d0.013
r_gen_planes_refined0.008
r_gen_planes_other0.004
r_bond_other_d0.002
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_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1005
Nucleic Acid Atoms
Solvent Atoms243
Heterogen Atoms40

Software

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