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Crystal structure of Lysosomal Phospholipase A2 in complex with Isopropyl dodec-11-enylfluorophosphonate (IDFP)
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 3.23 61.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.83 α = 79.08 b = 90.172 β = 88.88 c = 99.345 γ = 89.11
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 0.97933 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 2.28 30 98.2 0.08 0.113 0.08 6.9 2 95158
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 2.3 2.34 97.4 0.511 0.723 0.511 0.652 2
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 2.3 28.96 90314 4840 97.14 0.1849 0.1833 0.1883 0.2136 0.2149 RANDOM 35.152
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] 1.35 0.21 0.58 0.49 2.05 -0.96
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.545 r_dihedral_angle_1_deg 22.248 r_dihedral_angle_4_deg 13.078 r_dihedral_angle_3_deg 12.928 r_angle_refined_deg 1.52 r_angle_other_deg 1.239 r_chiral_restr 0.066 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.545 r_dihedral_angle_1_deg 22.248 r_dihedral_angle_4_deg 13.078 r_dihedral_angle_3_deg 12.928 r_angle_refined_deg 1.52 r_angle_other_deg 1.239 r_chiral_restr 0.066 r_bond_refined_d 0.008 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 12076 Nucleic Acid Atoms Solvent Atoms 513 Heterogen Atoms 498
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling SCALEPACK data scaling PHASER phasing Coot model building PDB_EXTRACT data extraction Aimless data scaling XDS data reduction