5GTP

The agonist-free structure of human PPARgamma ligand binding domain in the presence of the SRC-1 coactivator peptide


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3VN2 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP72962.2 M sodium malonate (pH 7.0)
Crystal Properties
Matthews coefficientSolvent content
2.7354.92

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 131.31α = 90
b = 53.062β = 90
c = 53.552γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2702014-05-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPAL/PLS BEAMLINE 7A (6B, 6C1)0.97934PAL/PLS7A (6B, 6C1)

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
12.355099.436.25.816193
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)
12.352.391000.60346.1

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 REPLACEMENTTHROUGHOUT3VN22.35301532881799.430.212920.210660.25809RANDOM67.958
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]
-2.540.821.71
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.648
r_dihedral_angle_4_deg22.439
r_dihedral_angle_3_deg14.4
r_long_range_B_refined11.45
r_long_range_B_other11.449
r_scangle_other8.449
r_mcangle_it7.147
r_mcangle_other7.145
r_dihedral_angle_1_deg5.614
r_scbond_it5.282
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.648
r_dihedral_angle_4_deg22.439
r_dihedral_angle_3_deg14.4
r_long_range_B_refined11.45
r_long_range_B_other11.449
r_scangle_other8.449
r_mcangle_it7.147
r_mcangle_other7.145
r_dihedral_angle_1_deg5.614
r_scbond_it5.282
r_scbond_other5.281
r_mcbond_it4.82
r_mcbond_other4.817
r_angle_refined_deg1.496
r_angle_other_deg1.181
r_chiral_restr0.082
r_bond_refined_d0.012
r_bond_other_d0.006
r_gen_planes_refined0.006
r_gen_planes_other0.002
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2196
Nucleic Acid Atoms
Solvent Atoms45
Heterogen Atoms22

Software

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