4X93

Crystal structure of Lysosomal Phospholipase A2 crystallized in the presence of methyl arachidonyl fluorophosphonate (tetragonal form)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4X90 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.5277100 mM HEPES pH 7.5, 30% PEG MME 550, 50 mM MgCl2
Crystal Properties
Matthews coefficientSolvent content
4.0169.36

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 86.82α = 90
b = 86.82β = 90
c = 365.848γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2013-06-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-D0.97933APS23-ID-D

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
12.6301000.1590.1650.0494.414.644707
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.62.641000.4280.76114.72205

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT4X902.63042161215899.790.19950.19860.2182RANDOM62.707
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]
0.670.67-1.34
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.107
r_dihedral_angle_3_deg12.608
r_dihedral_angle_4_deg11.2
r_dihedral_angle_1_deg5.914
r_mcangle_it2.542
r_mcbond_it1.484
r_mcbond_other1.484
r_angle_refined_deg1.24
r_angle_other_deg0.869
r_chiral_restr0.086
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.107
r_dihedral_angle_3_deg12.608
r_dihedral_angle_4_deg11.2
r_dihedral_angle_1_deg5.914
r_mcangle_it2.542
r_mcbond_it1.484
r_mcbond_other1.484
r_angle_refined_deg1.24
r_angle_other_deg0.869
r_chiral_restr0.086
r_bond_refined_d0.008
r_gen_planes_refined0.005
r_bond_other_d0.003
r_gen_planes_other0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6049
Nucleic Acid Atoms
Solvent Atoms91
Heterogen Atoms174

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
Aimlessdata scaling
PHASERphasing
Cootmodel building
PDB_EXTRACTdata extraction