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Design of peptide inhibitors of group II phospholipase A2: Crystal structure of the complex of phospholipsae A2 with a designed tripeptide, Ala- Tyr- Lys at 2.3 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4EIX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.2 298 0.3M AMMONIUM SULPHATE, 30% PEG 4000, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.45 49.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.166 α = 90 b = 53.166 β = 90 c = 48.548 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 2006-03-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU300 1.54
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 2.3 53.17 99.3 0.116 8.6 5887
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 2.3 2.38 100 0.368 2.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 4EIX 2.3 53.17 5723 275 98.15 0.20246 0.20246 0.20039 0.1994 0.24342 0.2628 RANDOM 27.953
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] 0.36 0.36 -0.73
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.484 r_dihedral_angle_3_deg 18.567 r_dihedral_angle_4_deg 8.259 r_dihedral_angle_1_deg 6.614 r_angle_refined_deg 2.23 r_chiral_restr 0.118 r_bond_refined_d 0.018 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 971 Nucleic Acid Atoms Solvent Atoms 98 Heterogen Atoms
Software Software Software Name Purpose HKL-2000 data collection AMoRE phasing REFMAC refinement AUTOMAR data reduction SCALEPACK data scaling