8ATY

Crystal structure of PPAR gamma (PPARG) in complex with JP85 (compound 1).


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6TSG 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8293.151.4 M Ammonium sulfate, 0.1 M tris pH 8.0
Crystal Properties
Matthews coefficientSolvent content
2.6353.21

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 65.331α = 90
b = 65.331β = 90
c = 156.041γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 2M2019-03-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06DA1.00000SLSX06DA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)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
11.944.399.30.0590.0650.0210.99916.68.727306
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.91.9798.50.8770.9870.3240.7672.28.5

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 REPLACEMENTTHROUGHOUT6TSG1.944.325886135398.990.17680.17550.201RANDOM43.145
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]
0.030.03-0.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.161
r_dihedral_angle_4_deg14.098
r_dihedral_angle_3_deg13.735
r_dihedral_angle_1_deg6.584
r_angle_refined_deg1.475
r_angle_other_deg1.383
r_chiral_restr0.08
r_bond_refined_d0.015
r_gen_planes_refined0.014
r_gen_planes_other0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.161
r_dihedral_angle_4_deg14.098
r_dihedral_angle_3_deg13.735
r_dihedral_angle_1_deg6.584
r_angle_refined_deg1.475
r_angle_other_deg1.383
r_chiral_restr0.08
r_bond_refined_d0.015
r_gen_planes_refined0.014
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2196
Nucleic Acid Atoms
Solvent Atoms155
Heterogen Atoms76

Software

Software
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing