4Y29

Identification of a novel PPARg ligand that regulates metabolism


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3U9Q 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP293.150.2 M Sodium thiocyanate, 20% w/v PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.3748.05

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 43.624α = 90
b = 54.514β = 107.07
c = 66.402γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2013-05-31MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL17U1.0050SSRFBL17U

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
11.985099.90.06811.65.321090
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)
11.982.011000.3565.21051

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 REPLACEMENTTHROUGHOUT3U9Q1.9841.3619842106899.940.17910.1770.2187RANDOM26.6
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]
-0.010.020.020.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.019
r_dihedral_angle_4_deg15.788
r_dihedral_angle_3_deg14.554
r_scangle_it6.77
r_dihedral_angle_1_deg5.853
r_scbond_it4.056
r_mcangle_it2.77
r_angle_refined_deg2.069
r_mcbond_it1.536
r_chiral_restr0.148
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.019
r_dihedral_angle_4_deg15.788
r_dihedral_angle_3_deg14.554
r_scangle_it6.77
r_dihedral_angle_1_deg5.853
r_scbond_it4.056
r_mcangle_it2.77
r_angle_refined_deg2.069
r_mcbond_it1.536
r_chiral_restr0.148
r_bond_refined_d0.026
r_gen_planes_refined0.01
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2135
Nucleic Acid Atoms
Solvent Atoms197
Heterogen Atoms26

Software

Software
Software NamePurpose
REFMACrefinement
SCALEPACKdata reduction
PHASERphasing
PDB_EXTRACTdata extraction