4L96

Structure of the complex between the F360L PPARgamma mutant and the ligand LT175 (space group I222)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3B3K 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.92930.35M Na-phosphate, 0.65 M K-phosphate., pH 6.9, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
3.564.86

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 67.17α = 90
b = 112β = 90
c = 116.8γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELPSI PILATUS 6M2013-05-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-1ESRFID23-1

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
12.38501000.1111.36.11795917959
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)
12.382.4999.30.6012.95.9

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 REPLACEMENTTHROUGHOUT3B3K2.3880.84176781701594499.870.185660.183480.22585RANDOM45.65
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]
1.25-0.18-1.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.069
r_dihedral_angle_4_deg16.257
r_dihedral_angle_3_deg14.74
r_mcangle_it6.294
r_dihedral_angle_1_deg5.949
r_scbond_it4.689
r_mcbond_other3.925
r_mcbond_it3.923
r_angle_refined_deg1.435
r_angle_other_deg0.786
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.069
r_dihedral_angle_4_deg16.257
r_dihedral_angle_3_deg14.74
r_mcangle_it6.294
r_dihedral_angle_1_deg5.949
r_scbond_it4.689
r_mcbond_other3.925
r_mcbond_it3.923
r_angle_refined_deg1.435
r_angle_other_deg0.786
r_chiral_restr0.074
r_bond_refined_d0.011
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
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_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2084
Nucleic Acid Atoms
Solvent Atoms126
Heterogen Atoms24

Software

Software
Software NamePurpose
REFMACrefinement
AMoREphasing
CNSrefinement
MOSFLMdata reduction
SCALAdata scaling
HKL-2000data collection