3N8X

Crystal Structure of Cyclooxygenase-1 in Complex with Nimesulide


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1Q4GPDB ENTRY 1Q4G

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.5273SODIUM CITRATE, LITHIUM CHLORIDE, SODIUM AZIDE, N-OCTYL GLUCOSIDE, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 273K
Crystal Properties
Matthews coefficientSolvent content
3.8768.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 181.709α = 90
b = 181.709β = 90
c = 103.454γ = 120
Symmetry
Space GroupP 65

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2008-07-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-FAPS21-ID-F

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
12.7929.696.80.08817.0426.8482001
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.752.8370

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)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 1Q4G2.7529.65031446907122795.50.1820.1810.227RANDOM56
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]
-1.67-1.673.34
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.964
r_dihedral_angle_4_deg20.868
r_dihedral_angle_3_deg19.137
r_dihedral_angle_1_deg6.191
r_scangle_it2.012
r_angle_refined_deg1.512
r_scbond_it1.263
r_mcangle_it0.808
r_mcbond_it0.426
r_chiral_restr0.095
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.964
r_dihedral_angle_4_deg20.868
r_dihedral_angle_3_deg19.137
r_dihedral_angle_1_deg6.191
r_scangle_it2.012
r_angle_refined_deg1.512
r_scbond_it1.263
r_mcangle_it0.808
r_mcbond_it0.426
r_chiral_restr0.095
r_bond_refined_d0.012
r_gen_planes_refined0.006
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 Atoms8867
Nucleic Acid Atoms
Solvent Atoms99
Heterogen Atoms341

Software

Software
Software NamePurpose
HKL-2000data collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling