2Q5P

Crystal Structure of PPARgamma bound to partial agonist MRL24


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
2.5852.36

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 91.355α = 90
b = 61.452β = 102.42
c = 117.947γ = 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
12.31591.70.0490.04925.46.3262182621849.23
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)
2.32.3863.50.1190.11910.44.41780

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 1KNU2.3102593725937127391.880.2080.2060.247RANDOM44.242
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]
-0.010.110.39-0.33
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.923
r_dihedral_angle_4_deg20.108
r_dihedral_angle_3_deg17.144
r_dihedral_angle_1_deg5.53
r_scangle_it2.235
r_scbond_it1.437
r_angle_refined_deg1.303
r_mcangle_it0.918
r_mcbond_it0.576
r_nbtor_refined0.305
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.923
r_dihedral_angle_4_deg20.108
r_dihedral_angle_3_deg17.144
r_dihedral_angle_1_deg5.53
r_scangle_it2.235
r_scbond_it1.437
r_angle_refined_deg1.303
r_mcangle_it0.918
r_mcbond_it0.576
r_nbtor_refined0.305
r_symmetry_vdw_refined0.223
r_nbd_refined0.216
r_symmetry_hbond_refined0.158
r_xyhbond_nbd_refined0.154
r_chiral_restr0.087
r_bond_refined_d0.011
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4047
Nucleic Acid Atoms
Solvent Atoms100
Heterogen Atoms76

Software

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