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The atomic resolution Crystal structure of the Phospholipase A2 (PLA2) complex with Nimesulide reveals its weaker binding to PLA2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1FB2 PDB ENTRY 1FB2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 298 0.2M Ammonium sulphate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.5 49.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.273 α = 90 b = 52.273 β = 90 c = 47.804 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 2005-03-24 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 1.1 52.2 99.8 0.06 18.2 51783 51691
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 1.12 99.9 0.372 2.3 3426
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 1FB2 1.1 52.2 51691 49031 2629 99.64 0.13242 0.13136 0.13014 0.1469 RANDOM 13.473
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] 0.05 0.05 -0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.452 r_dihedral_angle_3_deg 13.973 r_dihedral_angle_4_deg 7.337 r_sphericity_free 7.05 r_dihedral_angle_1_deg 6.104 r_scangle_it 4.447 r_scbond_it 3.801 r_sphericity_bonded 3.536 r_rigid_bond_restr 3.424 r_mcangle_it 2.892
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.452 r_dihedral_angle_3_deg 13.973 r_dihedral_angle_4_deg 7.337 r_sphericity_free 7.05 r_dihedral_angle_1_deg 6.104 r_scangle_it 4.447 r_scbond_it 3.801 r_sphericity_bonded 3.536 r_rigid_bond_restr 3.424 r_mcangle_it 2.892 r_mcbond_it 2.393 r_angle_refined_deg 1.668 r_angle_other_deg 0.914 r_mcbond_other 0.799 r_nbd_refined 0.405 r_symmetry_vdw_refined 0.359 r_symmetry_vdw_other 0.301 r_xyhbond_nbd_refined 0.247 r_nbd_other 0.213 r_nbtor_refined 0.2 r_symmetry_hbond_refined 0.173 r_chiral_restr 0.099 r_nbtor_other 0.095 r_bond_refined_d 0.016 r_gen_planes_refined 0.01 r_gen_planes_other 0.007 r_bond_other_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1012 Nucleic Acid Atoms Solvent Atoms 290 Heterogen Atoms 41
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling AMoRE phasing