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Design of specific inhibitors of phospholipase A2: Crystal structure of the complex formed between group I phospholipase A2 and a designed pentapeptide Leu-Ala-Ile-Tyr-Ser at 2.6A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1LFF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 298 10mM Sodium phosphate buffer, 35% Ethanol, 2mM Calcium chloride, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.1 43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.624 α = 90 b = 42.624 β = 90 c = 65.203 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 293 IMAGE PLATE MARRESEARCH Mirror 2003-06-04 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 2.6 20 100 0.108 6.8 5.6 3626 3626 47.7
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) 2.6 2.65 90.1 0.352 2
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 1LFF 2.6 19.36 3626 3306 176 90.9 0.256 0.191 0.191 0.232 RANDOM 37.3
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] -0.45 -0.45 0.9
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23.7 c_scangle_it 6.95 c_scbond_it 5.28 c_mcangle_it 4.02 c_mcbond_it 2.39 c_angle_deg 1.6 c_improper_angle_d 0.77 c_bond_d 0.007 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23.7 c_scangle_it 6.95 c_scbond_it 5.28 c_mcangle_it 4.02 c_mcbond_it 2.39 c_angle_deg 1.6 c_improper_angle_d 0.77 c_bond_d 0.007 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 952 Nucleic Acid Atoms Solvent Atoms 55 Heterogen Atoms 12
Software Software Software Name Purpose CNS refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing