5WZW

Crystal structure of human secreted phospholipase A2 group IIE with LY311727


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION2772.2M Sodium chloride, 0.1M BIS-TRIS propane pH 7.0
Crystal Properties
Matthews coefficientSolvent content
3.3963.67

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 48.853α = 90
b = 61.219β = 90
c = 63.325γ = 90
Symmetry
Space GroupP 21 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110CCDOXFORD RUBY CCD2013-05-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODEOXFORD DIFFRACTION ENHANCE ULTRA1.5406

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)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
11.9517.3899.80.0550.0620.0280.99719.64.514384
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.9521000.2130.2540.1360.9433.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT1.9517.381362670999.460.20660.20420.2552RANDOM19.838
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]
0.20.09-0.29
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.869
r_dihedral_angle_3_deg13.246
r_dihedral_angle_4_deg12.263
r_dihedral_angle_1_deg5.427
r_angle_refined_deg1.446
r_angle_other_deg1.143
r_chiral_restr0.12
r_bond_refined_d0.009
r_gen_planes_refined0.005
r_bond_other_d0.004
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.869
r_dihedral_angle_3_deg13.246
r_dihedral_angle_4_deg12.263
r_dihedral_angle_1_deg5.427
r_angle_refined_deg1.446
r_angle_other_deg1.143
r_chiral_restr0.12
r_bond_refined_d0.009
r_gen_planes_refined0.005
r_bond_other_d0.004
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms971
Nucleic Acid Atoms
Solvent Atoms163
Heterogen Atoms50

Software

Software
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction