2Q61

Crystal Structure of PPARgamma ligand binding domain bound to partial agonist SR145


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
2.652.68

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 90.131α = 90
b = 62.39β = 100.98
c = 117.93γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 325 mm CCDmirrorsMSINGLE 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
12.1972099.60.0660.06630.27.1327183271833.01
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)
12.1972.2899.40.50.420.0476.73251

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 1KNU2.1979.973237932379165099.390.190.1880.229RANDOM24.4
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]
-0.03-0.10.03-0.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.107
r_dihedral_angle_4_deg18.87
r_dihedral_angle_3_deg17.104
r_dihedral_angle_1_deg5.057
r_scangle_it2.818
r_scbond_it1.917
r_angle_refined_deg1.329
r_mcangle_it1.103
r_mcbond_it0.692
r_nbtor_refined0.305
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.107
r_dihedral_angle_4_deg18.87
r_dihedral_angle_3_deg17.104
r_dihedral_angle_1_deg5.057
r_scangle_it2.818
r_scbond_it1.917
r_angle_refined_deg1.329
r_mcangle_it1.103
r_mcbond_it0.692
r_nbtor_refined0.305
r_nbd_refined0.213
r_symmetry_vdw_refined0.181
r_xyhbond_nbd_refined0.16
r_symmetry_hbond_refined0.146
r_chiral_restr0.102
r_bond_refined_d0.013
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4075
Nucleic Acid Atoms
Solvent Atoms156
Heterogen Atoms54

Software

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