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Crystal Structure of Eicosapentanoic Acid Bound in the Cyclooxygenase Channel of Prostaglandin Endoperoxide H Synthase-1.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DIY pdb entry 1DIY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 lithium chloride, sodium azide, citric acid, n-octyl-glucoside, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K
Crystal Properties Matthews coefficient Solvent content 3.73 67.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 182.17 α = 90 b = 182.17 β = 90 c = 103.11 γ = 120
Symmetry Space Group P 65 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD CUSTOM-MADE 2000-08-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 1.03320 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 3.1 20 99.2 0.086 25.9 18711 18578
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.1 3.21 99.6 0.464 4.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT pdb entry 1DIY 3.1 20 2 16881 16196 685 90.2 0.228 0.2283 0.294 0.2933 4% of the total reflections were selected by CNS using the script make_cv.inp
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]
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22.021 c_angle_deg 1.5449 c_improper_angle_d 1.0584 c_bond_d 0.0102
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4383 Nucleic Acid Atoms Solvent Atoms 56 Heterogen Atoms 234
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling CNS refinement CNS phasing