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Crystal structure of Lysosomal Phospholipase A2 crystallized in the presence of methyl arachidonyl fluorophosphonate (tetragonal form)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4X90
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 277 100 mM HEPES pH 7.5, 30% PEG MME 550, 50 mM MgCl2
Crystal Properties Matthews coefficient Solvent content 4.01 69.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.82 α = 90 b = 86.82 β = 90 c = 365.848 γ = 90
Symmetry Space Group P 43 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARMOSAIC 300 mm CCD 2013-06-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 0.97933 APS 23-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) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.6 30 100 0.159 0.165 0.049 4.4 14.6 44707
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 2.64 100 0.428 0.761 14.7 2205
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4X90 2.6 30 42161 2158 99.79 0.1995 0.1986 0.2006 0.2182 0.2216 RANDOM 62.707
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] 0.67 0.67 -1.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.107 r_dihedral_angle_3_deg 12.608 r_dihedral_angle_4_deg 11.2 r_dihedral_angle_1_deg 5.914 r_mcangle_it 2.542 r_mcbond_it 1.484 r_mcbond_other 1.484 r_angle_refined_deg 1.24 r_angle_other_deg 0.869 r_chiral_restr 0.086
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.107 r_dihedral_angle_3_deg 12.608 r_dihedral_angle_4_deg 11.2 r_dihedral_angle_1_deg 5.914 r_mcangle_it 2.542 r_mcbond_it 1.484 r_mcbond_other 1.484 r_angle_refined_deg 1.24 r_angle_other_deg 0.869 r_chiral_restr 0.086 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d 0.003 r_gen_planes_other 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6049 Nucleic Acid Atoms Solvent Atoms 91 Heterogen Atoms 174
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling Aimless data scaling PHASER phasing Coot model building PDB_EXTRACT data extraction