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Crystal structure of fully glycosylated Lysosomal Phospholipase A2 in complex with methyl arachidonyl fluorophosphonate (MAFP)
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 3.5 297 100 mM Na citrate pH 3.5-4, 20% PEG 3350, and 100 mM NaCl
Crystal Properties Matthews coefficient Solvent content 3.7 66.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.385 α = 90 b = 125.275 β = 90 c = 140.215 γ = 90
Symmetry Space Group P 2 21 21
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 3.08 30 49.4 0.173 0.19 0.076 4.2 5.1 12079
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 3.1 3.15 4.5 0.342 0.423 0.244 0.783 2.6 54
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 3.08 30 11420 615 49.49 0.2195 0.2177 0.2037 0.2517 0.2433 RANDOM 150.015
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] 42.72 -17.63 -25.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.967 r_dihedral_angle_3_deg 14.549 r_dihedral_angle_4_deg 11.182 r_dihedral_angle_1_deg 4.998 r_mcangle_it 4.455 r_mcbond_it 2.627 r_mcbond_other 2.626 r_angle_refined_deg 1.02 r_angle_other_deg 0.746 r_chiral_restr 0.073
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.967 r_dihedral_angle_3_deg 14.549 r_dihedral_angle_4_deg 11.182 r_dihedral_angle_1_deg 4.998 r_mcangle_it 4.455 r_mcbond_it 2.627 r_mcbond_other 2.626 r_angle_refined_deg 1.02 r_angle_other_deg 0.746 r_chiral_restr 0.073 r_bond_refined_d 0.005 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6041 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 176
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling Aimless data scaling PHASER phasing Coot model building PDB_EXTRACT data extraction