2XKW

LIGAND BINDING DOMAIN OF HUMAN PPAR-GAMMA IN COMPLEX WITH THE AGONIST PIOGLITAZONE


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1PRGPDB ENTRY 1PRG

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION7.5292PROTEIN CONC. 17MG/ML, 50 MM TRIS PH 8.0,0.1M NACL, 0.5 MM DTT, 2 MM EDTA. RESERVOIR: 20% PEG4000,10% ISOPROPANOL, 0.1M HEPES PH 7.5 , VAPOR DIFFUSION,TEMPERATURE 292K
Crystal Properties
Matthews coefficientSolvent content
2.6152.93

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 92.861α = 90
b = 60.411β = 103.01
c = 119.849γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMARRESEARCHMIRRORS2005-01-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.2BESSY14.2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
12.012097.20.0418.33.13916834.8
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)
12.012.0863.10.292.52.4

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 REPLACEMENTTHROUGHOUTPDB ENTRY 1PRG2.022039168210497.20.1640.1620.202RANDOM33.61
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]
-0.820.092.2-1.34
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.686
r_dihedral_angle_4_deg16.245
r_dihedral_angle_3_deg15.56
r_scangle_it11.83
r_scbond_it9.432
r_mcangle_it5.959
r_dihedral_angle_1_deg5.199
r_mcbond_it4.856
r_mcbond_other1.66
r_angle_refined_deg1.36
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.686
r_dihedral_angle_4_deg16.245
r_dihedral_angle_3_deg15.56
r_scangle_it11.83
r_scbond_it9.432
r_mcangle_it5.959
r_dihedral_angle_1_deg5.199
r_mcbond_it4.856
r_mcbond_other1.66
r_angle_refined_deg1.36
r_angle_other_deg0.939
r_nbd_refined0.217
r_symmetry_vdw_refined0.205
r_nbtor_refined0.181
r_symmetry_vdw_other0.178
r_nbd_other0.163
r_xyhbond_nbd_refined0.132
r_chiral_restr0.105
r_symmetry_hbond_refined0.101
r_nbtor_other0.085
r_bond_refined_d0.012
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4145
Nucleic Acid Atoms
Solvent Atoms182
Heterogen Atoms78

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing