2Q6S

2.4 angstrom crystal structure of PPAR gamma complexed to BVT.13 without co-activator peptides


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1KNUPDB entry 1KNU

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP82981.4M sodium citrate, 0.125 M Tris 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.6453.41

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 92.348α = 90
b = 62.033β = 102.29
c = 118.132γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDmirrorsMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-ID0.9764APS22-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
12.41591.40.0560.05626.86.3232882328859.22
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.42.4959.10.1730.1730.07641486

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)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 1KNU2.4102298422984227390.580.2120.2060.264RANDOM40.708
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]
0.65-0.134.37-5.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.91
r_dihedral_angle_4_deg19.438
r_dihedral_angle_3_deg16.812
r_dihedral_angle_1_deg5.105
r_scangle_it4.999
r_scbond_it3.576
r_mcangle_it2.626
r_mcbond_it2.087
r_angle_refined_deg1.276
r_nbtor_refined0.303
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.91
r_dihedral_angle_4_deg19.438
r_dihedral_angle_3_deg16.812
r_dihedral_angle_1_deg5.105
r_scangle_it4.999
r_scbond_it3.576
r_mcangle_it2.626
r_mcbond_it2.087
r_angle_refined_deg1.276
r_nbtor_refined0.303
r_symmetry_vdw_refined0.246
r_nbd_refined0.217
r_xyhbond_nbd_refined0.216
r_symmetry_hbond_refined0.176
r_chiral_restr0.078
r_bond_refined_d0.012
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4061
Nucleic Acid Atoms
Solvent Atoms151
Heterogen Atoms27

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
MOLREPphasing