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Crystal Structure of the Complex Formed Between Phospholipase A2 and a Hexapeptide Fragment of Amyloid Beta Peptide, Lys-Leu-Val-Phe-Phe-Ala at 1.2 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 2.04 39.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.023 α = 90 b = 42.023 β = 90 c = 64.146 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 2009-03-30 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 1.2 42 95.9 0.036 7.9 34924 34924
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) 1.2 1.22 94.6 0.122 2.5
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 1.2 42 34924 31789 1695 96 0.18662 0.18076 0.2062 0.19284 0.2222 RANDOM 23.326
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] -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.328 r_dihedral_angle_3_deg 14.809 r_dihedral_angle_1_deg 5.236 r_dihedral_angle_4_deg 3.568 r_scangle_it 2.501 r_sphericity_bonded 2.36 r_sphericity_free 2.175 r_scbond_it 1.907 r_rigid_bond_restr 1.337 r_mcangle_it 1.302
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.328 r_dihedral_angle_3_deg 14.809 r_dihedral_angle_1_deg 5.236 r_dihedral_angle_4_deg 3.568 r_scangle_it 2.501 r_sphericity_bonded 2.36 r_sphericity_free 2.175 r_scbond_it 1.907 r_rigid_bond_restr 1.337 r_mcangle_it 1.302 r_angle_refined_deg 1.164 r_mcbond_it 0.833 r_nbtor_refined 0.306 r_symmetry_vdw_refined 0.269 r_nbd_refined 0.214 r_chiral_restr 0.081 r_xyhbond_nbd_refined 0.081 r_symmetry_hbond_refined 0.077 r_metal_ion_refined 0.034 r_bond_refined_d 0.007 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 960 Nucleic Acid Atoms Solvent Atoms 149 Heterogen Atoms 1
Software Software Software Name Purpose DENZO data reduction MOLREP phasing REFMAC refinement AUTOMAR data reduction SCALEPACK data scaling