3KRK

X-ray crystal structure of arachidonic acid bound in the cyclooxygenase channel of L531F murine COX-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, 0.1M Hepes pH 7.5, 0.02M MgCl2, VAPOR DIFFUSION, SITTING DROP, temperature 296K
Crystal Properties
Matthews coefficientSolvent content
2.6753.92

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 120.79α = 90
b = 133.04β = 90
c = 180.654γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102008-05-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCHESS BEAMLINE A10.9777CHESSA1

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
12.42096.80.17485.8551335513338.5
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)
2.42.5390.20.3222.12.47387

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 1CVU2.419.9225514352249279496.590.2260.18190.179480.2281RANDOM29.145
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]
0.810.18-0.99
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.949
r_dihedral_angle_3_deg14.383
r_dihedral_angle_4_deg13.405
r_dihedral_angle_1_deg5.058
r_scangle_it1.696
r_angle_refined_deg1.47
r_scbond_it0.957
r_mcangle_it0.522
r_mcbond_it0.26
r_chiral_restr0.119
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.949
r_dihedral_angle_3_deg14.383
r_dihedral_angle_4_deg13.405
r_dihedral_angle_1_deg5.058
r_scangle_it1.696
r_angle_refined_deg1.47
r_scbond_it0.957
r_mcangle_it0.522
r_mcbond_it0.26
r_chiral_restr0.119
r_bond_refined_d0.008
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8899
Nucleic Acid Atoms
Solvent Atoms632
Heterogen Atoms359

Software

Software
Software NamePurpose
XDSdata scaling
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling