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Design of specific inhibitors of groupII phospholipase A2(PLA2): Crystal structure of the complex formed between russells viper PLA2 and designed peptide Phe-Leu-Ala-Tyr-Lys at 1.7A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1SKG pdb entry 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 298K
Crystal Properties Matthews coefficient Solvent content 2.4 49.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.082 α = 90 b = 52.082 β = 90 c = 47.784 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 2004-04-25 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 52 99.7 0.041 16.4 12.3 14203 17.7
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) 1.7 1.73 99.6 0.177 4.4 704
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 1SKG 1.7 51.99 14203 13460 712 99.8 0.1699 0.16887 0.16746 0.19603 RANDOM 19.149
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] 0.1 0.1 -0.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.402 r_scangle_it 4.47 r_dihedral_angle_1_deg 3.919 r_scbond_it 2.886 r_mcangle_it 2.188 r_angle_refined_deg 2.18 r_angle_other_deg 1.287 r_mcbond_it 1.211 r_nbd_refined 0.434 r_symmetry_vdw_refined 0.384
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.402 r_scangle_it 4.47 r_dihedral_angle_1_deg 3.919 r_scbond_it 2.886 r_mcangle_it 2.188 r_angle_refined_deg 2.18 r_angle_other_deg 1.287 r_mcbond_it 1.211 r_nbd_refined 0.434 r_symmetry_vdw_refined 0.384 r_symmetry_vdw_other 0.38 r_nbd_other 0.254 r_xyhbond_nbd_refined 0.232 r_symmetry_hbond_refined 0.22 r_chiral_restr 0.183 r_xyhbond_nbd_other 0.073 r_bond_refined_d 0.019 r_gen_planes_refined 0.009 r_gen_planes_other 0.006 r_bond_other_d 0.001 r_dihedral_angle_2_deg r_dihedral_angle_4_deg r_nbtor_refined r_nbtor_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 990 Nucleic Acid Atoms Solvent Atoms 171 Heterogen Atoms 25
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing