5DSH

Human PPARgamma ligand binding dmain complexed with SB1406 in a covalent bonded form


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP72972.2M sodium malonate pH 7.0
Crystal Properties
Matthews coefficientSolvent content
2.6754.01

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.33α = 90
b = 131.332β = 90
c = 52.852γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2702014-12-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPAL/PLS BEAMLINE 7A (6B, 6C1)0.97934PAL/PLS7A (6B, 6C1)

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)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
12.955099.338.26.88258
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.9531004.67.1

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 DIFFRACTIONTHROUGHOUT2.9530786135999.180.207030.204770.25743RANDOM85.374
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]
-0.88-6.267.14
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.987
r_dihedral_angle_3_deg14.381
r_long_range_B_other11.332
r_long_range_B_refined11.33
r_dihedral_angle_4_deg9.819
r_scangle_other7.738
r_mcangle_it7.265
r_mcangle_other7.264
r_dihedral_angle_1_deg5.274
r_mcbond_it4.543
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.987
r_dihedral_angle_3_deg14.381
r_long_range_B_other11.332
r_long_range_B_refined11.33
r_dihedral_angle_4_deg9.819
r_scangle_other7.738
r_mcangle_it7.265
r_mcangle_other7.264
r_dihedral_angle_1_deg5.274
r_mcbond_it4.543
r_mcbond_other4.542
r_scbond_it4.5
r_scbond_other4.498
r_angle_refined_deg1.47
r_angle_other_deg0.887
r_chiral_restr0.065
r_gen_planes_refined0.016
r_gen_planes_other0.013
r_bond_refined_d0.009
r_bond_other_d0.006
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 Atoms2146
Nucleic Acid Atoms
Solvent Atoms25
Heterogen Atoms26

Software

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