2HFP

Crystal Structure of PPAR Gamma with N-sulfonyl-2-indole carboxamide ligands


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1298Two microliters of protein solution (10 mg/mL, 1 peptide fragment) was added to two microliters of well (2% Peg400, 1.6 Molar ammonium sulfate, 100 mM Mes 6.5) and hung over 1000 microliters well in a 2 + 2 hanging drop crystallization setup , temperature 298.0K
Crystal Properties
Matthews coefficientSolvent content
2.1141.67

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46.487α = 90
b = 77.178β = 90
c = 82.075γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2005-01-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-IDAPS22-ID

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
1239.82193.40.042716.830.93194331943325.7
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)
22.172.80.33423.480.732120

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT239.82074819404100593.530.2090.2090.2050.285RANDOM31.997
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]
1.61-0.52-1.09
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.379
r_dihedral_angle_3_deg18.238
r_dihedral_angle_4_deg16.531
r_dihedral_angle_1_deg13.646
r_scangle_it8.618
r_scbond_it5.873
r_mcangle_it3.741
r_mcbond_it2.638
r_angle_refined_deg1.808
r_chiral_restr0.438
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.379
r_dihedral_angle_3_deg18.238
r_dihedral_angle_4_deg16.531
r_dihedral_angle_1_deg13.646
r_scangle_it8.618
r_scbond_it5.873
r_mcangle_it3.741
r_mcbond_it2.638
r_angle_refined_deg1.808
r_chiral_restr0.438
r_symmetry_vdw_refined0.425
r_xyhbond_nbd_refined0.344
r_nbtor_refined0.327
r_nbd_refined0.28
r_symmetry_hbond_refined0.147
r_bond_refined_d0.017
r_gen_planes_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2326
Nucleic Acid Atoms
Solvent Atoms122
Heterogen Atoms80

Software

Software
Software NamePurpose
AMoREphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
SCALEPACKdata scaling