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X-ray crystal structure of arachidonic acid bound in the cyclooxygenase channel of G533V 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 2.71 54.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 122.265 α = 90 b = 133.508 β = 90 c = 181.093 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 2009-09-24 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 2.15 20 99.98 0.087 12.7 5.1 80417 76377
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 2.15 2.27 99.9 0.447 3.3 4.9
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 1CVU 2.15 19.99 80417 76377 4039 99.98 0.17179 0.16976 0.2033 0.2096 0.233 RANDOM 29.812
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] 1.01 0.06 -1.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.643 r_dihedral_angle_3_deg 14.109 r_dihedral_angle_4_deg 11.868 r_dihedral_angle_1_deg 5.44 r_scangle_it 2.321 r_scbond_it 1.39 r_angle_refined_deg 1.266 r_mcangle_it 0.665 r_mcbond_it 0.342 r_chiral_restr 0.086
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.643 r_dihedral_angle_3_deg 14.109 r_dihedral_angle_4_deg 11.868 r_dihedral_angle_1_deg 5.44 r_scangle_it 2.321 r_scbond_it 1.39 r_angle_refined_deg 1.266 r_mcangle_it 0.665 r_mcbond_it 0.342 r_chiral_restr 0.086 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8869 Nucleic Acid Atoms Solvent Atoms 816 Heterogen Atoms 343
Software Software Software Name Purpose Adxv data processing PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling