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Non-specific binding to phospholipase A2:Crystal structure of the complex of PLA2 with a designed peptide Tyr-Trp-Ala-Ala-Ala-Ala at 1.7A resolution
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 0.2M AMMONIUM SULPHATE, 30% PEG, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 2.5 50
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.29 α = 90 b = 52.29 β = 90 c = 47.81 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 200 CCD MARRESEARCH MIRROR 2004-05-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X11 0.806 EMBL/DESY, HAMBURG X11
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 1.7 51.99 100 0.057 27.8 24.8 355374 14306 17.71
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) 1.7 1.73 100 0.342 6.7 721
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 1SKG 1.7 51.99 14299 13580 719 99.97 0.1807 0.18028 0.17887 0.20615 RANDOM 17.915
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] 0.06 0.06 -0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.456 r_dihedral_angle_1_deg 3.803 r_scangle_it 3.422 r_scbond_it 2.132 r_angle_refined_deg 1.807 r_mcangle_it 1.653 r_angle_other_deg 0.971 r_mcbond_it 0.904 r_nbd_refined 0.441 r_symmetry_vdw_refined 0.283
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.456 r_dihedral_angle_1_deg 3.803 r_scangle_it 3.422 r_scbond_it 2.132 r_angle_refined_deg 1.807 r_mcangle_it 1.653 r_angle_other_deg 0.971 r_mcbond_it 0.904 r_nbd_refined 0.441 r_symmetry_vdw_refined 0.283 r_symmetry_vdw_other 0.254 r_nbd_other 0.22 r_symmetry_hbond_refined 0.21 r_xyhbond_nbd_refined 0.203 r_chiral_restr 0.091 r_xyhbond_nbd_other 0.031 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 r_gen_planes_other 0.004 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 990 Nucleic Acid Atoms Solvent Atoms 147 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing