8HHQ

Covalent bond formation between cysteine of PPARg-LBD and iodoacetic acid


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.42930.1 M Tris-HCl pH 7.4, 0.8 M sodium citrate
Crystal Properties
Matthews coefficientSolvent content
2.5151.09

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 92.142α = 90
b = 59.802β = 103.22
c = 117.956γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS II2017-08-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU R-AXIS II1.0

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)CC (Half)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
12.447.9396115.33.623224
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.42.490.9544

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 REPLACEMENTTHROUGHOUT2VV32.447.9322384120796.040.212740.209760.26627RANDOM38.559
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]
0.05-0.02-0.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.406
r_dihedral_angle_4_deg19.632
r_dihedral_angle_3_deg17.217
r_long_range_B_other7.66
r_long_range_B_refined7.651
r_dihedral_angle_1_deg5.689
r_scangle_other5.25
r_mcangle_it4.492
r_mcangle_other4.492
r_scbond_it3.36
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.406
r_dihedral_angle_4_deg19.632
r_dihedral_angle_3_deg17.217
r_long_range_B_other7.66
r_long_range_B_refined7.651
r_dihedral_angle_1_deg5.689
r_scangle_other5.25
r_mcangle_it4.492
r_mcangle_other4.492
r_scbond_it3.36
r_scbond_other3.359
r_mcbond_it2.914
r_mcbond_other2.904
r_angle_refined_deg1.527
r_angle_other_deg0.82
r_chiral_restr0.077
r_bond_refined_d0.013
r_bond_other_d0.006
r_gen_planes_refined0.006
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4023
Nucleic Acid Atoms
Solvent Atoms126
Heterogen Atoms8

Software

Software
Software NamePurpose
REFMACrefinement
d*TREKdata reduction
d*TREKdata scaling
PHASERphasing