4L98

Crystal structure of the complex of F360L PPARgamma mutant with the ligand LT175


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP72933.3 M Sodium Formate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
3.463.84

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 64.41α = 90
b = 112.46β = 90
c = 117.74γ = 90
Symmetry
Space GroupP 21 21 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 ID23-10.973ESRFID23-1

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
12.285099.90.08818.93971339713
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)
12.282.599.90.4244.8

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 REPLACEMENTTHROUGHOUT3B3K2.28117.743920437723195699.740.213090.210910.2576RANDOM43.074
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]
2.54-0.54-2
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.558
r_dihedral_angle_3_deg17.65
r_mcangle_it16.914
r_dihedral_angle_4_deg16.814
r_scbond_it12.487
r_mcbond_other10.935
r_mcbond_it10.933
r_dihedral_angle_1_deg6.348
r_angle_refined_deg1.506
r_angle_other_deg1.096
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.558
r_dihedral_angle_3_deg17.65
r_mcangle_it16.914
r_dihedral_angle_4_deg16.814
r_scbond_it12.487
r_mcbond_other10.935
r_mcbond_it10.933
r_dihedral_angle_1_deg6.348
r_angle_refined_deg1.506
r_angle_other_deg1.096
r_chiral_restr0.114
r_bond_refined_d0.011
r_gen_planes_refined0.007
r_bond_other_d0.004
r_gen_planes_other0.004
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 Atoms4015
Nucleic Acid Atoms
Solvent Atoms227
Heterogen Atoms48

Software

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