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Crystal structure of porcine pancreatic phospholipase A2 in complex with n-hexadecanoic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3O4M
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.2 294 15% MPD, 0.05M Tris Maliate, 5mM Calcium Chloride, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 3.44 64.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.26 α = 90 b = 69.26 β = 90 c = 69.66 γ = 120
Symmetry Space Group P 31 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 100 IMAGE PLATE MAR scanner 345 mm plate Mirrors 2010-02-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER AXS MICROSTAR 1.542
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.5 45.44 90.4 0.079 0.084 6866 6010 2.6 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 2.74 90.4
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3O4M 2.5 15 6866 5654 295 91.13 0.19411 0.19137 0.24935 0.2059 RANDOM 40.616
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 44.918 r_dihedral_angle_4_deg 26.11 r_dihedral_angle_3_deg 20.131 r_dihedral_angle_1_deg 6.62 r_scangle_it 5.023 r_scbond_it 2.906 r_mcangle_it 2.062 r_angle_refined_deg 1.898 r_mcbond_it 1.048 r_chiral_restr 0.132
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 44.918 r_dihedral_angle_4_deg 26.11 r_dihedral_angle_3_deg 20.131 r_dihedral_angle_1_deg 6.62 r_scangle_it 5.023 r_scbond_it 2.906 r_mcangle_it 2.062 r_angle_refined_deg 1.898 r_mcbond_it 1.048 r_chiral_restr 0.132 r_bond_refined_d 0.019 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 971 Nucleic Acid Atoms Solvent Atoms 58 Heterogen Atoms 20
Software Software Software Name Purpose MAR345dtb data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling