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Crystal Structure of Porcine Pancreatic Phospholipase A2 in Complex with 2-methoxycyclohexa-2-5-diene-1,4-dione
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1P2P PDB ENTRY 1P2P
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.2 294 15% MPD, 0.05M Tris Maleate, 5mM Calcium Chloride, pH7.2, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 3.38 63.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.36 α = 90 b = 68.36 β = 90 c = 70.12 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 2009-03-22 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 45.24 97.3 0.073 0.065 8.5 6789 6759 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 70.79 0.073 0.065 955
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 (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 1P2P 2.5 13.65 2 2.5 6811 6356 349 98.44 0.2303 0.18214 0.17965 0.2175 0.22883 0.2222 RANDOM 23.783
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 40.295 r_dihedral_angle_4_deg 28.049 r_dihedral_angle_3_deg 22.792 r_dihedral_angle_1_deg 7.137 r_scangle_it 4.224 r_scbond_it 2.545 r_angle_refined_deg 2.079 r_mcangle_it 1.644 r_mcbond_it 0.84 r_chiral_restr 0.135
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.295 r_dihedral_angle_4_deg 28.049 r_dihedral_angle_3_deg 22.792 r_dihedral_angle_1_deg 7.137 r_scangle_it 4.224 r_scbond_it 2.545 r_angle_refined_deg 2.079 r_mcangle_it 1.644 r_mcbond_it 0.84 r_chiral_restr 0.135 r_bond_refined_d 0.02 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 971 Nucleic Acid Atoms Solvent Atoms 32 Heterogen Atoms 12
Software Software Software Name Purpose MAR345dtb data collection Auto model building REFMAC refinement iMOSFLM data reduction SCALA data scaling Auto phasing