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Crystal structure of 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 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 2.84 56.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.147 α = 88.85 b = 85.495 β = 70.87 c = 88.852 γ = 79.74
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 2013-07-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 0.97857 APS 21-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 2.65 30 93.2 0.089 0.125 0.089 6.4 1.9 52162
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 2.65 2.7 4 0.573 0.81 0.573 0.222 1.2 111
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4X90 2.65 30 49603 2558 94.7 0.1813 0.1794 0.2191 0.1998 RANDOM 39.398
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] 1.3 1.46 -0.29 -1 -0.7 0.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.427 r_dihedral_angle_4_deg 15.994 r_dihedral_angle_3_deg 14.054 r_dihedral_angle_1_deg 6.16 r_mcangle_it 3.282 r_mcbond_it 2.018 r_mcbond_other 2.014 r_angle_refined_deg 1.788 r_angle_other_deg 1.262 r_chiral_restr 0.097
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.427 r_dihedral_angle_4_deg 15.994 r_dihedral_angle_3_deg 14.054 r_dihedral_angle_1_deg 6.16 r_mcangle_it 3.282 r_mcbond_it 2.018 r_mcbond_other 2.014 r_angle_refined_deg 1.788 r_angle_other_deg 1.262 r_chiral_restr 0.097 r_bond_refined_d 0.015 r_gen_planes_refined 0.009 r_bond_other_d 0.008 r_gen_planes_other 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12098 Nucleic Acid Atoms Solvent Atoms 232 Heterogen Atoms 372
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