2F4B

Crystal structure of the ligand binding domain of human PPAR-gamma in complex with an agonist


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP829120% PEG3350, 0.2 Sodium Citrate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.3246.87

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 55.967α = 90
b = 88.642β = 90.01
c = 57.878γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42005-05-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL12B21.0SPring-8BL12B2

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
12.073097.40.04634426
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.072.1497.4

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT2.073031791168797.160.222280.218590.28835RANDOM39.691
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]
1.14-0.65-0.95-0.19
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.615
r_dihedral_angle_4_deg18.918
r_dihedral_angle_3_deg18.428
r_dihedral_angle_1_deg7.022
r_scangle_it5.096
r_scbond_it3.83
r_mcbond_it1.967
r_angle_refined_deg1.919
r_symmetry_vdw_refined0.348
r_nbtor_refined0.314
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.615
r_dihedral_angle_4_deg18.918
r_dihedral_angle_3_deg18.428
r_dihedral_angle_1_deg7.022
r_scangle_it5.096
r_scbond_it3.83
r_mcbond_it1.967
r_angle_refined_deg1.919
r_symmetry_vdw_refined0.348
r_nbtor_refined0.314
r_nbd_refined0.241
r_xyhbond_nbd_refined0.194
r_symmetry_hbond_refined0.194
r_chiral_restr0.149
r_bond_refined_d0.021
r_gen_planes_refined0.01
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4356
Nucleic Acid Atoms
Solvent Atoms140
Heterogen Atoms39

Software

Software
Software NamePurpose
HKL-2000data collection
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
HKL-2000data reduction