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Exploitation of a Novel Binding Pocket in Human Lipoprotein-Associated Phospholipase A2 (Lp-PLA<sub>2</sub>) Discovered Through X-Ray Fragment Screening
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.4 297 1.0M NaCl, 0.1M HEPES/NaOHpH=7.4, 28.8%w/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.33 47.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.373 α = 90 b = 92.08 β = 112.6 c = 48.273 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 93 CCD RIGAKU SATURN 944+ 2010-06-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.12 46.33 99.2 7.5 3.6 21778
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 THROUGHOUT 2.12 46.33 21778 1172 99.2 0.22519 0.22291 0.2278 0.26693 0.2713 RANDOM 34.96
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] -2.67 0.78 -2.14 3.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.836 r_dihedral_angle_3_deg 14.233 r_dihedral_angle_4_deg 13.984 r_dihedral_angle_1_deg 6.805 r_long_range_B_refined 3.396 r_angle_refined_deg 1.425 r_scbond_it 1.347 r_scbond_other 1.347 r_mcbond_it 1.057 r_mcbond_other 1.036
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.836 r_dihedral_angle_3_deg 14.233 r_dihedral_angle_4_deg 13.984 r_dihedral_angle_1_deg 6.805 r_long_range_B_refined 3.396 r_angle_refined_deg 1.425 r_scbond_it 1.347 r_scbond_other 1.347 r_mcbond_it 1.057 r_mcbond_other 1.036 r_angle_other_deg 0.932 r_chiral_restr 0.082 r_bond_refined_d 0.011 r_bond_other_d 0.002 r_gen_planes_refined r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcangle_it r_mcangle_other r_scangle_it r_scangle_other r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2978 Nucleic Acid Atoms Solvent Atoms 131 Heterogen Atoms 18
Software Software Software Name Purpose REFMAC refinement d*TREK data reduction SCALA data scaling