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Indomethacin-(S)-alpha-ethyl-ethanolamide bound to Cyclooxygenase-1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DIY pdb entry 1diy (protein only)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 273 Sodium Citrate, Lithium Chloride, Sodium Azide, and beta-octylglucoside, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 273K
Crystal Properties Matthews coefficient Solvent content 3.81 67.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 181.41 α = 90 b = 181.41 β = 90 c = 103.398 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 MAR CCD 165 mm 2004-03-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 32-ID 1.0 APS 32-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 2.7 30 99.9 0.097 13 19 28072 28010 -3
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 2.7 2.76 100 0.335 15 1834
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT pdb entry 1diy (protein only) 2.7 30 28072 27878 1400 99.55 0.241 0.241 0.3203 0.292 0.3516 RANDOM 51.256
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] 0.94 0.47 0.94 -1.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.495 r_dihedral_angle_3_deg 20.021 r_dihedral_angle_4_deg 18.336 r_dihedral_angle_1_deg 6.412 r_scangle_it 1.665 r_angle_refined_deg 1.52 r_scbond_it 1.005 r_mcangle_it 0.656 r_mcbond_it 0.371 r_nbtor_refined 0.324
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.495 r_dihedral_angle_3_deg 20.021 r_dihedral_angle_4_deg 18.336 r_dihedral_angle_1_deg 6.412 r_scangle_it 1.665 r_angle_refined_deg 1.52 r_scbond_it 1.005 r_mcangle_it 0.656 r_mcbond_it 0.371 r_nbtor_refined 0.324 r_nbd_refined 0.243 r_symmetry_vdw_refined 0.23 r_symmetry_hbond_refined 0.213 r_xyhbond_nbd_refined 0.147 r_chiral_restr 0.094 r_bond_refined_d 0.011 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4408 Nucleic Acid Atoms Solvent Atoms 52 Heterogen Atoms 192
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction MAR345 data collection MOLREP phasing