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Design of specific inhibitors of Phopholipase A2: Crystal structure of the complex formed between Group II Phopholipase A2 and a designed peptide Dehydro-Ile-Ala-Arg-Ser at 1.2A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1FB2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.8 297 0.2M Ammonium sulphate,50% PEG, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 297K
Crystal Properties Matthews coefficient Solvent content 2.5 50
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.549 α = 90 b = 52.549 β = 90 c = 47.833 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 203 CCD MARRESEARCH MIRROR 2003-09-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X31 0.803 EMBL/DESY, HAMBURG X31
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 1.2 20 99.5 0.082 17.3 19.4 40325 40325 10.3
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 1.2 1.24 100 0.09 14
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 1FB2 1.2 17.68 40325 39501 824 100 0.2147 0.20949 0.20934 0.21705 RANDOM 14.267
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] 0.21 0.21 -0.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.249 r_dihedral_angle_1_deg 2.917 r_scangle_it 2.452 r_scbond_it 1.66 r_angle_refined_deg 1.542 r_mcangle_it 1.401 r_angle_other_deg 0.833 r_mcbond_it 0.779 r_nbd_refined 0.409 r_symmetry_vdw_other 0.323
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.249 r_dihedral_angle_1_deg 2.917 r_scangle_it 2.452 r_scbond_it 1.66 r_angle_refined_deg 1.542 r_mcangle_it 1.401 r_angle_other_deg 0.833 r_mcbond_it 0.779 r_nbd_refined 0.409 r_symmetry_vdw_other 0.323 r_symmetry_vdw_refined 0.3 r_symmetry_hbond_refined 0.239 r_nbd_other 0.216 r_xyhbond_nbd_refined 0.163 r_chiral_restr 0.086 r_xyhbond_nbd_other 0.039 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 r_gen_planes_other 0.005 r_bond_other_d 0.002 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 984 Nucleic Acid Atoms Solvent Atoms 270 Heterogen Atoms 15
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling AMoRE phasing