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Interactions of a specific non-steroidal anti-inflammatory drug (NSAID) with group I phospholipase A2 (PLA2): Crystal structure of the complex formed between PLA2 and niflumic acid at 2.5 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1MF4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 293 10mM Sodium Phosphate, 2mM CaCl2, 25% Ethanol, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.1 41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.356 α = 90 b = 42.356 β = 90 c = 64.958 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 monochromator 2004-04-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X11 0.80200 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 2.5 20 99.7 0.063 20.6 4004 4004
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) 2.5 2.59 99.5 0.238 7.5 4004
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 1MF4 2.5 20 4004 4004 179 99.73 0.211 0.19481 0.19262 0.24203 RANDOM 27.425
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] -0.46 -0.46 0.93
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.921 r_scangle_it 3.411 r_dihedral_angle_1_deg 2.382 r_scbond_it 2.06 r_angle_refined_deg 1.812 r_mcangle_it 1.507 r_angle_other_deg 0.932 r_mcbond_it 0.769 r_nbd_refined 0.321 r_symmetry_vdw_other 0.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.921 r_scangle_it 3.411 r_dihedral_angle_1_deg 2.382 r_scbond_it 2.06 r_angle_refined_deg 1.812 r_mcangle_it 1.507 r_angle_other_deg 0.932 r_mcbond_it 0.769 r_nbd_refined 0.321 r_symmetry_vdw_other 0.305 r_symmetry_vdw_refined 0.289 r_nbd_other 0.231 r_symmetry_hbond_refined 0.214 r_xyhbond_nbd_refined 0.172 r_chiral_restr 0.1 r_xyhbond_nbd_other 0.041 r_bond_refined_d 0.015 r_gen_planes_refined 0.005 r_gen_planes_other 0.003 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 914 Nucleic Acid Atoms Solvent Atoms 101 Heterogen Atoms 21
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing