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Crystal structure of Lysosomal Phospholipase A2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 277 100 mM HEPES pH 7.5, 3.5% PEG 8000, 28% MPD, 300 mM (NH4)2HPO4
Crystal Properties Matthews coefficient Solvent content 3.28 62.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.806 α = 78.13 b = 91.151 β = 88.46 c = 100.266 γ = 88.5
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) 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 1.83 30 97.8 0.095 6.7 4 183439
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.83 1.86 96.4 0.631 3.9 8966
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.84 30 174210 9229 96.85 0.155 0.1541 0.1652 0.1733 0.1827 RANDOM 26.422
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] 1.71 -0.24 0.13 -0.22 0.2 -1.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.364 r_dihedral_angle_4_deg 13.245 r_dihedral_angle_3_deg 11.529 r_dihedral_angle_1_deg 5.816 r_mcangle_it 2.04 r_angle_refined_deg 1.441 r_mcbond_it 1.271 r_mcbond_other 1.271 r_angle_other_deg 1.168 r_chiral_restr 0.085
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.364 r_dihedral_angle_4_deg 13.245 r_dihedral_angle_3_deg 11.529 r_dihedral_angle_1_deg 5.816 r_mcangle_it 2.04 r_angle_refined_deg 1.441 r_mcbond_it 1.271 r_mcbond_other 1.271 r_angle_other_deg 1.168 r_chiral_restr 0.085 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_bond_other_d 0.006 r_gen_planes_other 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12076 Nucleic Acid Atoms Solvent Atoms 1065 Heterogen Atoms 476
Software Software Software Name Purpose HKL-2000 data reduction HKL-2000 data scaling PHASER phasing Coot model building REFMAC refinement PDB_EXTRACT data extraction