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Crystal structure of Lysosomal Phospholipase A2-S165A
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 6.5 277 100 mM Na cacodylate pH 6.5, 10% PEG 8000, 200 mM Mg(CH3COO) in the presence of DOPC liposomes
Crystal Properties Matthews coefficient Solvent content 4.13 70.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 257.239 α = 90 b = 257.239 β = 90 c = 257.239 γ = 90
Symmetry Space Group F 41 3 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 3 30 98.7 0.217 0.23 0.098 3.9 5.6 14922
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3 3.05 100 0.93 0.428 0.605 5.6 722
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 3 30 14138 764 98.45 0.19 0.1883 0.1929 0.2203 0.2143 RANDOM 43.389
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.809 r_dihedral_angle_4_deg 18.705 r_dihedral_angle_3_deg 15.78 r_dihedral_angle_1_deg 6.003 r_mcangle_it 2.094 r_angle_refined_deg 1.349 r_mcbond_it 1.225 r_mcbond_other 1.219 r_angle_other_deg 0.775 r_chiral_restr 0.077
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.809 r_dihedral_angle_4_deg 18.705 r_dihedral_angle_3_deg 15.78 r_dihedral_angle_1_deg 6.003 r_mcangle_it 2.094 r_angle_refined_deg 1.349 r_mcbond_it 1.225 r_mcbond_other 1.219 r_angle_other_deg 0.775 r_chiral_restr 0.077 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3029 Nucleic Acid Atoms Solvent Atoms 20 Heterogen Atoms 56
Software Software Software Name Purpose HKL-2000 data scaling PHASER phasing Coot model building REFMAC refinement PDB_EXTRACT data extraction