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Crystal structure of porcine pancreatic phospholipase A2 in complex with 1,2-dihydroxybenzene
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.2 294 5% MPD, 0.05M Tris Maleate, 5mM Calcium Chloride, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 294.0K
Crystal Properties Matthews coefficient Solvent content 3.44 64.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.24 α = 90 b = 69.24 β = 90 c = 69.67 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 2010-04-02 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) 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 59.96 95.07 0.092 6960 6617 2.5 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.64 95.07 0.092 0.032
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) 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 2.5 19.99 2 2.5 979 6617 326 99.76 0.18355 0.1816 0.2271 0.22257 0.25 RANDOM 42.261
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 42.333 r_dihedral_angle_4_deg 21.195 r_dihedral_angle_3_deg 16.928 r_dihedral_angle_1_deg 6.502 r_scangle_it 4.83 r_scbond_it 2.933 r_angle_refined_deg 1.803 r_mcangle_it 1.791 r_mcbond_it 0.911 r_chiral_restr 0.126
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.333 r_dihedral_angle_4_deg 21.195 r_dihedral_angle_3_deg 16.928 r_dihedral_angle_1_deg 6.502 r_scangle_it 4.83 r_scbond_it 2.933 r_angle_refined_deg 1.803 r_mcangle_it 1.791 r_mcbond_it 0.911 r_chiral_restr 0.126 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 56 Heterogen Atoms 10
Software Software Software Name Purpose MAR345dtb data collection Auto model building REFMAC refinement MOSFLM data reduction SCALA data scaling Auto phasing