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Design of specific peptide inhibitors of phospholipase A2: Crystal structure of the complex formed between a group II phospholipase A2 and a designed pentapeptide Ala- Leu- Val- Tyr- Lys at 2.3 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1FB2 1FB2.pdb
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.2 298 0.2M ammonium sulphate, 30% PEG 4000, pH 7.2, VAPOR DIFFUSION, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.41 48.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.14 α = 90 b = 53.14 β = 90 c = 48.53 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 288 IMAGE PLATE MARRESEARCH Mirror 2006-03-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU300
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 2.3 20 97.7 5989 5989 37.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.3 2.34 94.7
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1FB2.pdb 2.3 18.79 5989 5924 336 97 0.21 0.21 0.197 0.1998 0.212 0.1992 RANDOM 30.8
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] 1.41 1.41 -2.82
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23.9 c_scangle_it 2.56 c_angle_deg 2.2 c_mcangle_it 2.04 c_scbond_it 1.68 c_mcbond_it 1.18 c_improper_angle_d 1.13 c_bond_d 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 985 Nucleic Acid Atoms Solvent Atoms 109 Heterogen Atoms 5
Software Software Software Name Purpose CNS refinement AUTOMAR data reduction DENZO data reduction SCALEPACK data scaling AMoRE phasing