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X-ray crystal structure of arachidonic acid bound to the cyclooxygenase channel of R513H murine COX-2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1CVU PDB entry 1CVU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 296 23-34% polyacrylic acid 5100, 100mM HEPES pH 7.5, 20mM MgCl2, VAPOR DIFFUSION, SITTING DROP, temperature 296K
Crystal Properties Matthews coefficient Solvent content 2.66 53.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 121.148 α = 90 b = 132.048 β = 90 c = 180.758 γ = 90
Symmetry Space Group I 2 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 ADSC QUANTUM 210 2009-04-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CHESS BEAMLINE A1 0.9780 CHESS A1
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 2.45 20 99.8 0.099 11.8 4.9 53369 53369 -3 -6 43.5
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 2.45 2.58 100 0.536 2.7 4.9 7699
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-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 1CVU 2.45 19.86 -6 53369 50659 2707 100 0.16565 0.16281 0.1823 0.21929 0.231 RANDOM 30.636
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] 0.81 0.26 -1.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.549 r_dihedral_angle_3_deg 15.352 r_dihedral_angle_4_deg 14.24 r_dihedral_angle_1_deg 5.511 r_scangle_it 3.127 r_scbond_it 1.907 r_angle_refined_deg 1.663 r_mcangle_it 0.957 r_mcbond_it 0.483 r_chiral_restr 0.095
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.549 r_dihedral_angle_3_deg 15.352 r_dihedral_angle_4_deg 14.24 r_dihedral_angle_1_deg 5.511 r_scangle_it 3.127 r_scbond_it 1.907 r_angle_refined_deg 1.663 r_mcangle_it 0.957 r_mcbond_it 0.483 r_chiral_restr 0.095 r_bond_refined_d 0.013 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8865 Nucleic Acid Atoms Solvent Atoms 513 Heterogen Atoms 368
Software Software Software Name Purpose Adxv data processing PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling