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Crystal Structure of the Complex Formed Between a New Isoform of Phospholipase A2 with C-terminal Amyloid Beta Heptapeptide 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 10mM Sodium phosphate, pH 6.0, 1mM CaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal Properties Matthews coefficient Solvent content 2.19 43.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.679 α = 90 b = 42.679 β = 90 c = 65.817 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 2008-09-23 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 2.04 20 97.6 0.115 7.8 7596 7596
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 2.04 2.09 96.7 0.305 2.1
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 (All) 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 2.04 19.51 7596 7065 340 97.91 0.19 0.18606 0.18436 0.1995 0.22137 0.2225 RANDOM 28.418
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] -0.43 -0.43 0.87
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.77 r_dihedral_angle_3_deg 15.611 r_dihedral_angle_4_deg 13.796 r_dihedral_angle_1_deg 4.884 r_scangle_it 2.944 r_scbond_it 1.878 r_mcangle_it 1.408 r_angle_refined_deg 1.172 r_mcbond_it 0.732 r_symmetry_hbond_refined 0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.77 r_dihedral_angle_3_deg 15.611 r_dihedral_angle_4_deg 13.796 r_dihedral_angle_1_deg 4.884 r_scangle_it 2.944 r_scbond_it 1.878 r_mcangle_it 1.408 r_angle_refined_deg 1.172 r_mcbond_it 0.732 r_symmetry_hbond_refined 0.3 r_nbtor_refined 0.299 r_symmetry_vdw_refined 0.274 r_nbd_refined 0.203 r_xyhbond_nbd_refined 0.175 r_chiral_restr 0.103 r_metal_ion_refined 0.013 r_bond_refined_d 0.012 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 949 Nucleic Acid Atoms Solvent Atoms 93 Heterogen Atoms 1
Software Software Software Name Purpose DENZO data reduction MOLREP phasing REFMAC refinement AUTOMAR data reduction SCALEPACK data scaling