1SXK

Crystal Structure of a complex formed between phospholipase A2 and a non-specific anti-inflammatory amino salicylic acid at 1.2 A resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1FB2 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.82970.2M ammonium sulphate, 50% PEG, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 297K
Crystal Properties
Matthews coefficientSolvent content
2.550

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 52.255α = 90
b = 52.255β = 90
c = 47.743γ = 90
Symmetry
Space GroupP 43

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray200CCDMARRESEARCHMirrors2003-09-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X110.8030EMBL/DESY, HAMBURGX11

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
11.2201000.06710.110.2384663846611.6
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)
1.21.231000.2223.7

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 REPLACEMENTTHROUGHOUT1FB21.2118.4738466384668081000.173880.173880.173560.18845RANDOM12.873
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]
0.080.08-0.16
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg19.321
r_dihedral_angle_1_deg4.904
r_angle_refined_deg1.646
r_scangle_it1.547
r_scbond_it0.849
r_angle_other_deg0.846
r_mcangle_it0.767
r_nbd_refined0.406
r_mcbond_it0.384
r_symmetry_vdw_refined0.298
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg19.321
r_dihedral_angle_1_deg4.904
r_angle_refined_deg1.646
r_scangle_it1.547
r_scbond_it0.849
r_angle_other_deg0.846
r_mcangle_it0.767
r_nbd_refined0.406
r_mcbond_it0.384
r_symmetry_vdw_refined0.298
r_symmetry_vdw_other0.271
r_nbd_other0.204
r_xyhbond_nbd_refined0.204
r_symmetry_hbond_refined0.183
r_chiral_restr0.08
r_bond_refined_d0.006
r_gen_planes_refined0.004
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_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms944
Nucleic Acid Atoms
Solvent Atoms222
Heterogen Atoms31

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing