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Phospholipase A2 Prevents the Aggregation of Amyloid Beta Peptides: Crystal Structure of the Complex of Phospholipase A2 with Octapeptide Fragment of Amyloid Beta Peptide, Asp-Ala-Glu-Phe-Arg-His-Asp-Ser at 2 A Resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1MF4 PDB ENTRY 1MF4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 290 calcium chloride, sodium phosphate, PH6.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal Properties Matthews coefficient Solvent content 2.14 42.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.795 α = 90 b = 42.795 β = 90 c = 65.832 γ = 90
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 300 IMAGE PLATE MARRESEARCH MIRROR 2009-01-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU300 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (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 2.03 20 98.7 0.07 11.1 7735 7735
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.03 2.06 87.7 0.188 4.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 PDB ENTRY 1MF4 2.03 20 7735 7256 351 98.86 0.18458 0.18188 0.1963 0.22063 0.2388 RANDOM 24.881
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] -0.5 -0.5 1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.818 r_dihedral_angle_3_deg 15.48 r_dihedral_angle_4_deg 14.415 r_dihedral_angle_1_deg 5.061 r_scangle_it 2.77 r_scbond_it 1.908 r_mcangle_it 1.412 r_angle_refined_deg 1.137 r_mcbond_it 0.739 r_symmetry_hbond_refined 0.453
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.818 r_dihedral_angle_3_deg 15.48 r_dihedral_angle_4_deg 14.415 r_dihedral_angle_1_deg 5.061 r_scangle_it 2.77 r_scbond_it 1.908 r_mcangle_it 1.412 r_angle_refined_deg 1.137 r_mcbond_it 0.739 r_symmetry_hbond_refined 0.453 r_nbtor_refined 0.303 r_symmetry_vdw_refined 0.283 r_nbd_refined 0.218 r_xyhbond_nbd_refined 0.132 r_metal_ion_refined 0.103 r_chiral_restr 0.084 r_bond_refined_d 0.009 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 977 Nucleic Acid Atoms Solvent Atoms 99 Heterogen Atoms 1
Software Software Software Name Purpose DENZO data reduction MOLREP phasing REFMAC refinement AUTOMAR data reduction SCALEPACK data scaling