3S9S

Ligand binding domain of PPARgamma complexed with a benzimidazole partial agonist


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2POBPDB entry 2POB

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.5298100MM HEPES, 1.4M SODIUM CITRATE, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.2344.83

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 56.086α = 90
b = 88.754β = 90
c = 122.605γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102007-06-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 17-IDAPS17-ID

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
12.5561.395.90.05847.65.69418941822
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)
12.552.61850.4455

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 2POB2.5561.329418941847795.90.2270.2240.284RANDOM71.789
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]
1.91.41-3.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.597
r_dihedral_angle_4_deg18.106
r_dihedral_angle_3_deg14.841
r_dihedral_angle_1_deg4.678
r_scangle_it1.799
r_angle_refined_deg1.158
r_scbond_it1.102
r_mcangle_it0.709
r_mcbond_it0.379
r_chiral_restr0.069
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.597
r_dihedral_angle_4_deg18.106
r_dihedral_angle_3_deg14.841
r_dihedral_angle_1_deg4.678
r_scangle_it1.799
r_angle_refined_deg1.158
r_scbond_it1.102
r_mcangle_it0.709
r_mcbond_it0.379
r_chiral_restr0.069
r_bond_refined_d0.009
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 Atoms2095
Nucleic Acid Atoms
Solvent Atoms52
Heterogen Atoms31

Software

Software
Software NamePurpose
ADSCdata collection
AMoREphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling