7CXG

The ligand-free structure of human PPARgamma LBD Q286E mutant


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6L8B 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52951.2 M Sodium citrate tribasic dihydrate, 0.1 M HEPES pH 7.5
Crystal Properties
Matthews coefficientSolvent content
2.4449.66

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 91.986α = 90
b = 59.886β = 103.399
c = 117.761γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M-F2018-02-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE AR-NE3A1.0000Photon FactoryAR-NE3A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)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
11.885099.90.9922.495.251089
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.881.910.751.96

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE6L8B1.8849.81850005259298.2340.1890.18660.230821.622
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]
-0.0270.064-0.0750.064
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.644
r_dihedral_angle_4_deg16.617
r_dihedral_angle_3_deg13.068
r_dihedral_angle_1_deg5.371
r_lrange_it5.009
r_lrange_other5.009
r_scangle_it2.784
r_scangle_other2.783
r_mcangle_it2.063
r_mcangle_other2.063
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.644
r_dihedral_angle_4_deg16.617
r_dihedral_angle_3_deg13.068
r_dihedral_angle_1_deg5.371
r_lrange_it5.009
r_lrange_other5.009
r_scangle_it2.784
r_scangle_other2.783
r_mcangle_it2.063
r_mcangle_other2.063
r_scbond_it1.681
r_scbond_other1.68
r_angle_other_deg1.278
r_mcbond_it1.253
r_mcbond_other1.25
r_angle_refined_deg1.226
r_symmetry_nbd_refined0.248
r_nbd_refined0.204
r_symmetry_xyhbond_nbd_refined0.186
r_nbd_other0.185
r_symmetry_nbd_other0.175
r_xyhbond_nbd_refined0.163
r_nbtor_refined0.155
r_symmetry_nbtor_other0.082
r_chiral_restr0.067
r_gen_planes_refined0.005
r_bond_refined_d0.004
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4257
Nucleic Acid Atoms
Solvent Atoms296
Heterogen Atoms18

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing