4OJ4

Crystal structure of V290M PPARgamma mutant in complex with diclofenac


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.5291PEG 4000 30%, CaCl2 200 mM, HEPES 100 mM, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.2946.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.04α = 90
b = 60.04β = 90
c = 161.19γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2011-11-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.11.0ALS5.0.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
12.356.26493.20.1520.1527.87.212961129613
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.32.421000.6250.6251.27.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT2.348.19129611221064392.870.22240.21940.2837RANDOM47.487
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]
3.113.11-6.23
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.43
r_dihedral_angle_4_deg15.968
r_dihedral_angle_3_deg15.581
r_dihedral_angle_1_deg6.279
r_angle_refined_deg1.638
r_angle_other_deg0.966
r_chiral_restr0.084
r_bond_refined_d0.013
r_gen_planes_other0.009
r_gen_planes_refined0.008
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.43
r_dihedral_angle_4_deg15.968
r_dihedral_angle_3_deg15.581
r_dihedral_angle_1_deg6.279
r_angle_refined_deg1.638
r_angle_other_deg0.966
r_chiral_restr0.084
r_bond_refined_d0.013
r_gen_planes_other0.009
r_gen_planes_refined0.008
r_bond_other_d0.002
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_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2026
Nucleic Acid Atoms
Solvent Atoms58
Heterogen Atoms21

Software

Software
Software NamePurpose
REFMACrefinement
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
MOSFLMdata reduction
SCALAdata scaling