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Identification of a potent anti-inflammatory agent from the natural extract of plant Cardiospermun helicacabum: Crystal structure of the complex of phospholipase A2 with Benzo(g)-1,3-benzodioxolo(5,6-a)quinolizinium, 5,6-dihydro-9,10-dimethoxy at 1.93 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2PYC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.8 298 50mm Ammonium acetate, 0.2M ammonium sulphate, 30%PEG 4000, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.52 51.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.311 α = 90 b = 53.311 β = 90 c = 48.379 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 291 IMAGE PLATE MAR scanner 345 mm plate Mirror 2007-08-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU300 1.54132
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 1.93 53.45 99.2 10240 9715
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 1.93 2 95.3
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2PYC 1.93 53.45 10240 9715 490 98.9 0.21 0.17765 0.1754 0.22435 0.2695 RANDOM 32.511
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] 0.47 0.47 -0.95
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.245 r_scangle_it 4.476 r_dihedral_angle_1_deg 4.474 r_scbond_it 2.834 r_mcangle_it 2.116 r_angle_refined_deg 1.802 r_mcbond_it 1.137 r_symmetry_vdw_refined 0.448 r_nbd_refined 0.371 r_xyhbond_nbd_refined 0.216
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.245 r_scangle_it 4.476 r_dihedral_angle_1_deg 4.474 r_scbond_it 2.834 r_mcangle_it 2.116 r_angle_refined_deg 1.802 r_mcbond_it 1.137 r_symmetry_vdw_refined 0.448 r_nbd_refined 0.371 r_xyhbond_nbd_refined 0.216 r_symmetry_hbond_refined 0.193 r_chiral_restr 0.108 r_bond_refined_d 0.017 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_dihedral_angle_2_deg r_dihedral_angle_4_deg r_gen_planes_other r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 943 Nucleic Acid Atoms Solvent Atoms 112 Heterogen Atoms 25
Software Software Software Name Purpose REFMAC refinement MAR345dtb data collection DENZO data reduction SCALEPACK data scaling AMoRE phasing