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Simultaneous inhibition of anti-coagulation and inflammation: Crystal structure of phospholipase A2 complexed with indomethacin at 1.4 A resolution reveals the presence of the new common ligand binding site
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1SKG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 298 0.3M AMMONIUM SULPHATE, 30% PEG 4000, pH 7.00, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.4 48.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.66 α = 90 b = 51.66 β = 90 c = 48.003 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 298 IMAGE PLATE MARRESEARCH Mirror 2006-10-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU300 1.5414
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.4 51.99 99.2 0.045 19.5 19.7 24939 24939 21.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.4 1.42 100 0.418 2.9
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1SKG 1.4 51.99 24939 23491 1262 99.2 0.19042 0.188 0.188 0.2115 0.202 0.2208 RANDOM 22.37
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] 0.34 0.34 -0.68
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.907 r_dihedral_angle_1_deg 2.317 r_scangle_it 2.081 r_angle_refined_deg 1.675 r_scbond_it 1.304 r_mcangle_it 1.116 r_angle_other_deg 0.755 r_mcbond_it 0.604 r_nbd_refined 0.395 r_nbd_other 0.232
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.907 r_dihedral_angle_1_deg 2.317 r_scangle_it 2.081 r_angle_refined_deg 1.675 r_scbond_it 1.304 r_mcangle_it 1.116 r_angle_other_deg 0.755 r_mcbond_it 0.604 r_nbd_refined 0.395 r_nbd_other 0.232 r_symmetry_vdw_other 0.207 r_symmetry_hbond_refined 0.204 r_xyhbond_nbd_refined 0.189 r_symmetry_vdw_refined 0.124 r_xyhbond_nbd_other 0.083 r_chiral_restr 0.08 r_symmetry_hbond_other 0.008 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_gen_planes_other 0.002 r_bond_other_d 0.001 r_dihedral_angle_2_deg r_dihedral_angle_4_deg r_nbtor_refined r_nbtor_other r_metal_ion_refined r_metal_ion_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 998 Nucleic Acid Atoms Solvent Atoms 224 Heterogen Atoms 45
Software Software Software Name Purpose HKL-2000 data collection AMoRE phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling