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Crystal structure of Lysosomal Phospholipase A2 crystallized in the presence of methyl arachidonyl fluorophosphonate (hexagonal 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, HANGING DROP 3 277 100 mM citric acid pH 3, 0.8 M ammonium sulfate ; crystallized in the presence of methyl arachidonyl fluorophosphonate
Crystal Properties Matthews coefficient Solvent content 3.23 61.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.978 α = 90 b = 95.978 β = 90 c = 207.943 γ = 120
Symmetry Space Group P 62 2 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 0.97937 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 2.7 30 94.7 0.134 0.139 0.036 7.8 12.5 16438
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) Redundancy Number Unique Reflections (All) 1 2.7 2.74 92.4 0.75 0.78 0.203 0.905 11.6 765
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 2.7 30 15534 853 99.66 0.1793 0.177 0.1847 0.2211 0.2243 RANDOM 50.566
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] 1.09 0.54 1.09 -3.52
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.436 r_dihedral_angle_3_deg 15.236 r_dihedral_angle_4_deg 13.713 r_dihedral_angle_1_deg 6.437 r_mcangle_it 2.906 r_mcbond_it 1.752 r_mcbond_other 1.752 r_angle_refined_deg 1.408 r_angle_other_deg 0.806 r_chiral_restr 0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.436 r_dihedral_angle_3_deg 15.236 r_dihedral_angle_4_deg 13.713 r_dihedral_angle_1_deg 6.437 r_mcangle_it 2.906 r_mcbond_it 1.752 r_mcbond_other 1.752 r_angle_refined_deg 1.408 r_angle_other_deg 0.806 r_chiral_restr 0.09 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3019 Nucleic Acid Atoms Solvent Atoms 34 Heterogen Atoms 96
Software Software Software Name Purpose HKL-2000 data scaling SCALEPACK data scaling Aimless data scaling Coot model building PHASER phasing REFMAC refinement PDB_EXTRACT data extraction