6TSG

Crystal structure of Peroxisome proliferator-activated receptor gamma (PPARG) in complex with TETRAC


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP293.1533% PEG 3350 and 0.15 M sodium citrate
Crystal Properties
Matthews coefficientSolvent content
2.550.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 61.678α = 90
b = 61.678β = 90
c = 166.487γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2019-03-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06DA1.0000SLSX06DA

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
12.9841.6299.30.0840.0990.0380.99913.76.37082
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)
12.983.1499.90.9721.1370.4290.6081.86.7

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 REPLACEMENTTHROUGHOUT6avi2.9841.62667535698.960.23950.23650.2924RANDOM103.512
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]
1.721.72-3.44
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.085
r_dihedral_angle_4_deg17.21
r_dihedral_angle_3_deg15.845
r_dihedral_angle_1_deg6.833
r_angle_other_deg1.148
r_angle_refined_deg1.136
r_chiral_restr0.053
r_bond_refined_d0.011
r_gen_planes_refined0.011
r_gen_planes_other0.003
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.085
r_dihedral_angle_4_deg17.21
r_dihedral_angle_3_deg15.845
r_dihedral_angle_1_deg6.833
r_angle_other_deg1.148
r_angle_refined_deg1.136
r_chiral_restr0.053
r_bond_refined_d0.011
r_gen_planes_refined0.011
r_gen_planes_other0.003
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2057
Nucleic Acid Atoms
Solvent Atoms4
Heterogen Atoms22

Software

Software
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing