5YCP

Human PPARgamma ligand binding domain complexed with Rosiglitazone


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5GTO 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP72962.2 M sodium malonate (pH 7.0)
Crystal Properties
Matthews coefficientSolvent content
2.7755.65

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 130.809α = 90
b = 53.133β = 90
c = 54.57γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2015-11-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPAL/PLS BEAMLINE 5C (4A)0.97960PAL/PLS5C (4A)

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
125099.953.49.9

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 REPLACEMENTTHROUGHOUT5GTO23025141131799.870.202870.201320.23338RANDOM44.458
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]
-0.91.13-0.23
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.001
r_dihedral_angle_4_deg21.224
r_dihedral_angle_3_deg13.649
r_long_range_B_refined8.097
r_long_range_B_other8.095
r_scangle_other6.243
r_dihedral_angle_1_deg5.545
r_mcangle_it4.553
r_mcangle_other4.553
r_scbond_it3.952
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.001
r_dihedral_angle_4_deg21.224
r_dihedral_angle_3_deg13.649
r_long_range_B_refined8.097
r_long_range_B_other8.095
r_scangle_other6.243
r_dihedral_angle_1_deg5.545
r_mcangle_it4.553
r_mcangle_other4.553
r_scbond_it3.952
r_scbond_other3.95
r_angle_other_deg3.51
r_mcbond_it3.167
r_mcbond_other3.166
r_angle_refined_deg1.486
r_chiral_restr0.091
r_bond_refined_d0.012
r_gen_planes_other0.008
r_gen_planes_refined0.007
r_bond_other_d
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2206
Nucleic Acid Atoms
Solvent Atoms85
Heterogen Atoms25

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing