5WZT

Crystal structure of human secreted phospholipase A2 group IIE with Compound 14


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5WZM 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION2772.2M Sodium chloride, 0.1M BIS-TRIS propane pH 7.0
Crystal Properties
Matthews coefficientSolvent content
3.3663.43

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 48.93α = 90
b = 60.676β = 90
c = 63.379γ = 90
Symmetry
Space GroupP 21 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110CCDOXFORD RUBY CCD2014-09-25MSINGLE 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
12.418.4799.80.1230.130.0420.99716.89.27799
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)
12.42.491000.6040.6360.1960.88910.2

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 REPLACEMENTTHROUGHOUT5WZM2.418.47740537399.480.2210.21860.2674RANDOM32.773
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]
-1.263.04-1.78
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.108
r_dihedral_angle_3_deg17.142
r_dihedral_angle_4_deg15.653
r_dihedral_angle_1_deg5.38
r_angle_refined_deg1.421
r_angle_other_deg0.944
r_chiral_restr0.074
r_bond_refined_d0.011
r_gen_planes_refined0.007
r_bond_other_d0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.108
r_dihedral_angle_3_deg17.142
r_dihedral_angle_4_deg15.653
r_dihedral_angle_1_deg5.38
r_angle_refined_deg1.421
r_angle_other_deg0.944
r_chiral_restr0.074
r_bond_refined_d0.011
r_gen_planes_refined0.007
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms971
Nucleic Acid Atoms
Solvent Atoms50
Heterogen Atoms39

Software

Software
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
CrysalisProdata reduction