2POB

PPARgamma Ligand binding domain complexed with a farglitazar analogue gw4709


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherPPARgamma lbd

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.5298100mM Hepes and 1.4M sodium citrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.6854.05

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 92.916α = 90
b = 62.006β = 101.94
c = 118.172γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray1002000-10-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 17-ID1.0APS17-ID

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
12.324.591.10.0520.05222.974.52945426825-3-349.8
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)
12.32.3865.30.4830.4831.612.42940

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 REPLACEMENTTHROUGHOUTPPARgamma lbd2.324.52592387590.990.226120.22450.27302RANDOM59.851
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]
-0.33-0.39-0.350.51
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.04
r_dihedral_angle_4_deg21.435
r_dihedral_angle_3_deg16.844
r_dihedral_angle_1_deg6.227
r_scangle_it2.179
r_scbond_it1.483
r_angle_refined_deg1.265
r_mcangle_it0.939
r_angle_other_deg0.9
r_mcbond_it0.58
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.04
r_dihedral_angle_4_deg21.435
r_dihedral_angle_3_deg16.844
r_dihedral_angle_1_deg6.227
r_scangle_it2.179
r_scbond_it1.483
r_angle_refined_deg1.265
r_mcangle_it0.939
r_angle_other_deg0.9
r_mcbond_it0.58
r_symmetry_hbond_refined0.234
r_nbd_refined0.216
r_symmetry_vdw_refined0.199
r_nbd_other0.183
r_symmetry_vdw_other0.183
r_nbtor_refined0.18
r_xyhbond_nbd_refined0.157
r_mcbond_other0.11
r_nbtor_other0.087
r_chiral_restr0.066
r_xyhbond_nbd_other0.03
r_bond_refined_d0.013
r_gen_planes_refined0.004
r_bond_other_d0.002
r_gen_planes_other0.001
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3962
Nucleic Acid Atoms
Solvent Atoms221
Heterogen Atoms49

Software

Software
Software NamePurpose
REFMACrefinement
MAR345data collection
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing