2Q5S

Crystal Structure of PPARgamma bound to partial agonist nTZDpa


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1KNUPDB Entry 1KNU

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP82981.4M sodium citrate, 0.125M Tris8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.5852.31

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 89.712α = 90
b = 62.194β = 101.05
c = 117.956γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 325 mm CCDmirrorMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL11-10.9537SSRLBL11-1

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
12.052099.30.0550.05533.46.9399123991230.79
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)
12.052.1295.30.3440.3443.44.43805

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB Entry 1KNU2.059.973957139571199299.290.1990.1970.245RANDOM24.836
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]
-0.03-0.040.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.616
r_dihedral_angle_4_deg20.696
r_dihedral_angle_3_deg16.439
r_dihedral_angle_1_deg10.701
r_scangle_it2.415
r_scbond_it1.767
r_angle_refined_deg1.354
r_mcangle_it1.02
r_mcbond_it0.857
r_symmetry_hbond_refined0.458
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.616
r_dihedral_angle_4_deg20.696
r_dihedral_angle_3_deg16.439
r_dihedral_angle_1_deg10.701
r_scangle_it2.415
r_scbond_it1.767
r_angle_refined_deg1.354
r_mcangle_it1.02
r_mcbond_it0.857
r_symmetry_hbond_refined0.458
r_nbtor_refined0.305
r_symmetry_vdw_refined0.256
r_nbd_refined0.213
r_xyhbond_nbd_refined0.169
r_chiral_restr0.147
r_bond_refined_d0.01
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4052
Nucleic Acid Atoms
Solvent Atoms264
Heterogen Atoms56

Software

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