2FVJ

A novel anti-adipogenic partial agonist of peroxisome proliferator-activated receptor-gamma (PPARG) recruits pparg-coactivator-1 alpha (PGC1A) but potentiates insulin signaling in vitro


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
otherIN HOUSE PPARG STRUCTURE

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.529320% PEG3350, 0.2M magnesium chloride, 0.1M Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.3748.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.483α = 90
b = 65.897β = 90
c = 87.538γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2004-07-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06SA0.7997SLSX06SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.993099.62171621716
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.0797.4

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTIN HOUSE PPARG STRUCTURE1.99302157521575110599.60.192250.192250.189420.24586RANDOM35.317
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]
-0.111.84-1.73
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.59
r_dihedral_angle_4_deg17.156
r_dihedral_angle_3_deg16.511
r_dihedral_angle_1_deg5.444
r_scangle_it4.18
r_scbond_it2.709
r_mcangle_it1.78
r_angle_refined_deg1.582
r_mcbond_it1.096
r_nbtor_refined0.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.59
r_dihedral_angle_4_deg17.156
r_dihedral_angle_3_deg16.511
r_dihedral_angle_1_deg5.444
r_scangle_it4.18
r_scbond_it2.709
r_mcangle_it1.78
r_angle_refined_deg1.582
r_mcbond_it1.096
r_nbtor_refined0.31
r_symmetry_hbond_refined0.29
r_symmetry_vdw_refined0.227
r_nbd_refined0.221
r_xyhbond_nbd_refined0.193
r_chiral_restr0.125
r_bond_refined_d0.015
r_gen_planes_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2149
Nucleic Acid Atoms
Solvent Atoms253
Heterogen Atoms46

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling