3HS7

X-ray crystal structure of docosahexaenoic acid bound to the cyclooxygenase channel of cyclooxygenase-2


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1CVUPDB entry 1CVU

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.529623-34% Polyacrylic acid 5100, 100mM HEPES pH 7.5, 20mM MgCl2, VAPOR DIFFUSION, SITTING DROP, temperature 296K
Crystal Properties
Matthews coefficientSolvent content
2.5952.53

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 119.294α = 90
b = 131.708β = 90
c = 179.243γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102008-12-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCHESS BEAMLINE A10.9789CHESSA1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.652099.80.12410.95.94120550.4
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.652.791000.4893.45.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 1CVU2.65204120520741000.183660.180990.23404RANDOM38.339
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]
2.37-0.09-2.28
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.367
r_dihedral_angle_3_deg14.63
r_dihedral_angle_4_deg12.259
r_dihedral_angle_1_deg4.735
r_scangle_it1.426
r_angle_refined_deg1.021
r_scbond_it0.763
r_mcangle_it0.401
r_mcbond_it0.196
r_chiral_restr0.073
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.367
r_dihedral_angle_3_deg14.63
r_dihedral_angle_4_deg12.259
r_dihedral_angle_1_deg4.735
r_scangle_it1.426
r_angle_refined_deg1.021
r_scbond_it0.763
r_mcangle_it0.401
r_mcbond_it0.196
r_chiral_restr0.073
r_bond_refined_d0.006
r_gen_planes_refined0.004
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 AtomsNumber
Protein Atoms8841
Nucleic Acid Atoms
Solvent Atoms330
Heterogen Atoms372

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
Adxvdata processing
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing