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Structure-based design of potent and selective inhibitors of phospholipase A2: Crystal structure of the complex formed between phosholipase A2 from Naja Naja sagittifera and a designed peptide inhibitor at 1.9 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1LN8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6 295 sodium phosphate, CaCl2, ethanol; Co-crystallation of protein: peptide in 1:10 molar ratio, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K, pH 6.00
Crystal Properties Matthews coefficient Solvent content 2.26 45.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.779 α = 90 b = 42.779 β = 90 c = 65.866 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 290 IMAGE PLATE MARRESEARCH MONOCHROMATOR 2001-06-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200
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 1.9 20 93.2 0.073 19.3 1.04 8247 -3 20.63
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 1.9 1.97 61.3 0.289 1.9
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 (Observed) R-Work (Depositor) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1LN8 1.9 19.54 8247 8247 411 100 0.184 0.182 0.239 RANDOM 25.5
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] -0.24 -0.24 0.49
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 17.004 r_dihedral_angle_3_deg 17.004 r_scangle_it 3.903 r_dihedral_angle_1_deg 3.468 r_scbond_it 2.472 r_mcangle_it 1.769 r_angle_refined_deg 1.748 r_mcbond_it 0.88 r_symmetry_hbond_refined 0.689 r_symmetry_vdw_refined 0.449
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 17.004 r_dihedral_angle_3_deg 17.004 r_scangle_it 3.903 r_dihedral_angle_1_deg 3.468 r_scbond_it 2.472 r_mcangle_it 1.769 r_angle_refined_deg 1.748 r_mcbond_it 0.88 r_symmetry_hbond_refined 0.689 r_symmetry_vdw_refined 0.449 r_nbd_refined 0.292 r_xyhbond_nbd_refined 0.167 r_chiral_restr 0.109 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_dihedral_angle_4_deg r_gen_planes_other r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 950 Nucleic Acid Atoms Solvent Atoms 105 Heterogen Atoms 1
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling AMoRE phasing REFMAC refinement