8CPH

Crystal structure of PPAR gamma (PPARG) in complex with WY-14643 (inactive form)


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP293.1530% PEG 3350, 0.15M sodium citrate
Crystal Properties
Matthews coefficientSolvent content
2.6353.27

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 62.521α = 90
b = 63.355β = 90
c = 168.355γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2021-12-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06SA1.00002SLSX06SA

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
12.444.599.80.0580.0630.02117.29.626908
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)
12.42.511.2551.4090.4550.7381.89.4

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT2.444.5425555129899.680.218860.216380.26341RANDOM89.352
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]
3.231.6-4.83
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.818
r_dihedral_angle_4_deg17.642
r_dihedral_angle_3_deg16.585
r_long_range_B_refined10.028
r_long_range_B_other10.028
r_scangle_other7.603
r_dihedral_angle_1_deg7.222
r_mcangle_it6.484
r_mcangle_other6.483
r_scbond_it5.106
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.818
r_dihedral_angle_4_deg17.642
r_dihedral_angle_3_deg16.585
r_long_range_B_refined10.028
r_long_range_B_other10.028
r_scangle_other7.603
r_dihedral_angle_1_deg7.222
r_mcangle_it6.484
r_mcangle_other6.483
r_scbond_it5.106
r_scbond_other5.104
r_mcbond_it4.438
r_mcbond_other4.437
r_angle_refined_deg1.326
r_angle_other_deg1.2
r_chiral_restr0.06
r_bond_refined_d0.011
r_gen_planes_refined0.01
r_bond_other_d0.003
r_gen_planes_other0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4222
Nucleic Acid Atoms
Solvent Atoms36
Heterogen Atoms42

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing