8CPJ

Crystal structure of PPAR gamma (PPARG) in an inactive form


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP293.1527% PEG 3350, 0.15M sodium citrate
Crystal Properties
Matthews coefficientSolvent content
2.6453.44

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 63.106α = 90
b = 63.106β = 90
c = 168.056γ = 90
Symmetry
Space GroupP 41 21 2

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
12.444.621000.1010.1070.0290.99919.613.814070
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)
12.42.481.3871.4960.3940.798214.2

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 REPLACEMENTTHROUGHOUT2.444.661333767499.960.240640.238350.28194RANDOM96.467
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]
1.631.63-3.27
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.836
r_dihedral_angle_4_deg17.539
r_dihedral_angle_3_deg14.871
r_long_range_B_other14.012
r_long_range_B_refined14.011
r_scangle_other10.114
r_mcangle_it9.612
r_mcangle_other9.609
r_dihedral_angle_1_deg6.901
r_scbond_it6.67
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.836
r_dihedral_angle_4_deg17.539
r_dihedral_angle_3_deg14.871
r_long_range_B_other14.012
r_long_range_B_refined14.011
r_scangle_other10.114
r_mcangle_it9.612
r_mcangle_other9.609
r_dihedral_angle_1_deg6.901
r_scbond_it6.67
r_scbond_other6.667
r_mcbond_it6.565
r_mcbond_other6.548
r_angle_refined_deg1.122
r_angle_other_deg1.059
r_chiral_restr0.043
r_bond_refined_d0.012
r_gen_planes_refined0.007
r_bond_other_d0.002
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 Atoms2158
Nucleic Acid Atoms
Solvent Atoms14
Heterogen Atoms12

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing