5GTN

Human PPARgamma ligand binding dmain complexed with R35


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3VN2 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP729657.5% (v/v) Tacsimate pH7.0
Crystal Properties
Matthews coefficientSolvent content
2.9157.66

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 131.65α = 90
b = 52.454β = 90
c = 54.289γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2702013-10-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPAL/PLS BEAMLINE 7A (6B, 6C1)1.00000PAL/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
11.855099.739.54.832794
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.851.881000.43734.8

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 REPLACEMENTTHROUGHOUT3VN21.853031197154999.60.205940.204620.23165RANDOM39.063
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]
-0.810.86-0.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.948
r_dihedral_angle_4_deg20.086
r_dihedral_angle_3_deg12.802
r_long_range_B_refined7.741
r_long_range_B_other7.487
r_dihedral_angle_1_deg5.397
r_scangle_other4.899
r_mcangle_it3.982
r_mcangle_other3.98
r_scbond_it3.009
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.948
r_dihedral_angle_4_deg20.086
r_dihedral_angle_3_deg12.802
r_long_range_B_refined7.741
r_long_range_B_other7.487
r_dihedral_angle_1_deg5.397
r_scangle_other4.899
r_mcangle_it3.982
r_mcangle_other3.98
r_scbond_it3.009
r_scbond_other3.008
r_mcbond_other2.612
r_mcbond_it2.611
r_angle_refined_deg1.488
r_angle_other_deg0.981
r_chiral_restr0.077
r_bond_refined_d0.011
r_gen_planes_refined0.006
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 Atoms2265
Nucleic Acid Atoms
Solvent Atoms210
Heterogen Atoms45

Software

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