2Q6R

Crystal structure of PPAR gamma complexed with partial agonist SF147


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 Tris 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.6152.96

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 90.8α = 90
b = 62.255β = 101.12
c = 118.071γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDmirrorsMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-ID0.9764APS22-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
12.41591.30.0680.06824.66.3229112291157.39
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)
2.42.4956.80.1960.1964.83.31413

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 1KNU2.407102264222642114690.910.270.2690.284RANDOM88.97
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]
0.690.076.03-6.69
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.929
r_dihedral_angle_3_deg18.73
r_dihedral_angle_4_deg16.954
r_dihedral_angle_1_deg12.592
r_scangle_it10.973
r_mcangle_it9.548
r_scbond_it6.915
r_mcbond_it5.593
r_angle_refined_deg1.616
r_xyhbond_nbd_refined0.322
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.929
r_dihedral_angle_3_deg18.73
r_dihedral_angle_4_deg16.954
r_dihedral_angle_1_deg12.592
r_scangle_it10.973
r_mcangle_it9.548
r_scbond_it6.915
r_mcbond_it5.593
r_angle_refined_deg1.616
r_xyhbond_nbd_refined0.322
r_nbtor_refined0.306
r_nbd_refined0.234
r_chiral_restr0.228
r_symmetry_vdw_refined0.189
r_symmetry_hbond_refined0.142
r_bond_refined_d0.009
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3887
Nucleic Acid Atoms
Solvent Atoms124
Heterogen Atoms58

Software

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