6IZN

Crystal structure of the PPARgamma-LBD complexed with compound 3g


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3V9T 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.5295PEG 4000, NaSCN, Tris-HCl
Crystal Properties
Matthews coefficientSolvent content
2.0439.84

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 38.994α = 90
b = 54.353β = 92.6
c = 66.594γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray93IMAGE PLATERIGAKU RAXIS IV2008-04-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E DW1.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.7550980.05524.17.52787624.3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.751.81930.2593.6

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 REPLACEMENTTHROUGHOUT3V9T1.7519.6627679278598.20.2390.2360.265RANDOM25
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]
5.46-3.55-1.93-3.53
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d18.2
c_scangle_it2.53
c_scbond_it1.76
c_mcangle_it1.66
c_mcbond_it1.1
c_angle_deg0.7
c_improper_angle_d0.61
c_bond_d0.004
c_bond_d_na
c_bond_d_prot
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d18.2
c_scangle_it2.53
c_scbond_it1.76
c_mcangle_it1.66
c_mcbond_it1.1
c_angle_deg0.7
c_improper_angle_d0.61
c_bond_d0.004
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2205
Nucleic Acid Atoms
Solvent Atoms159
Heterogen Atoms31

Software

Software
Software NamePurpose
CNXrefinement
HKL-2000data reduction
HKL-2000data scaling
CNXphasing