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Crystal structure of porcine pancreatic phospholipase A2 complexed with berberine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4P2P PDB ENTRY 4P2P
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.2 293 0.05M Tris maleate buffer, 5mM CaCl2, 16% MPD, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.4 63.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.6 α = 90 b = 68.6 β = 90 c = 70.08 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 2009-03-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU300 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 2.3 49 98.1 7686
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 4P2P 2.3 9.9 7686 391 93.16 0.18767 0.18455 0.1984 0.25313 0.2687 RANDOM 45.444
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 0.01 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.398 r_dihedral_angle_4_deg 28.948 r_dihedral_angle_3_deg 19.241 r_dihedral_angle_1_deg 6.741 r_scangle_it 4.056 r_scbond_it 2.558 r_angle_refined_deg 1.796 r_mcangle_it 1.698 r_mcbond_it 0.907 r_chiral_restr 0.114
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.398 r_dihedral_angle_4_deg 28.948 r_dihedral_angle_3_deg 19.241 r_dihedral_angle_1_deg 6.741 r_scangle_it 4.056 r_scbond_it 2.558 r_angle_refined_deg 1.796 r_mcangle_it 1.698 r_mcbond_it 0.907 r_chiral_restr 0.114 r_bond_refined_d 0.018 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 971 Nucleic Acid Atoms Solvent Atoms 106 Heterogen Atoms 27
Software Software Software Name Purpose MAR345dtb data collection REFMAC refinement MOSFLM data reduction SCALA data scaling