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Design of specific inhibitors of Phospholipase A2: Crystal structure of the complex of phospholipase A2 with pentapeptide Leu-Val-Phe-Phe-Ala at 2.9 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1S6B PDB ENTRY 1S6B
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 295 calcium chloride, tris, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.32 46.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.54 α = 90 b = 65.54 β = 90 c = 58.551 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 300 IMAGE PLATE MARRESEARCH Mirror 2007-06-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU300 1.5418
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 2.97 20 98.8 0.179 5.5 4980 4980
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) 2.97 3.08 97.5 0.465 1.7
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 Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1S6B 2.97 20 4980 4710 270 98.7 0.2585 0.2576 0.2512 0.2735 RANDOM 30.3
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] -2.83 -2.83 5.66
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 24 c_angle_deg 1.4 c_bond_d 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1880 Nucleic Acid Atoms Solvent Atoms 58 Heterogen Atoms 2
Software Software Software Name Purpose DENZO data reduction AMoRE phasing CNS refinement AUTOMAR data reduction SCALEPACK data scaling