5KYJ

Brain penetrant liver X receptor (LXR) modulators based on a 2,4,5,6-tetrahydropyrrolo[3,4-c]pyrazole core


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP82981uL of scLXRbeta-LBD/scRXRbeta-LBD @ 10 mg protein/ml in 20 mM Tris-HCl pH 8.0, 150 mM NaCl, 5 mM DTT containing 1mM ligand and less than 2%(v/v) DMSO was mixed with 1uL of reservoir solution (0.2M LiCl, 16-20%(w/v) PEG3350, 7-10%(v/v) ethylene glycol, 0.01M Strontium chloride) on a circular, silanized glass cover slide and inverted and sealed with silicon grease over a well of 200uL of reservoir solution. Crystallization plates were incubated at 23 deg C for 2-5 days before rods would appear measuring 50 to 100um long.
Crystal Properties
Matthews coefficientSolvent content
2.1241.98

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 69.92α = 90
b = 100.93β = 90
c = 145.9γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2012-02-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X29A1.075NSLSX29A

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
12.843.8199.8219.47.62477056.6
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.82.87299.572.477.8

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 REPLACEMENTTHROUGHOUT5I4V2.843.8124770129099.820.201340.198650.2528RANDOM56.58
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]
-0.070.040.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.073
r_dihedral_angle_4_deg19.61
r_dihedral_angle_3_deg17.558
r_long_range_B_refined9.377
r_long_range_B_other9.376
r_scangle_other7.121
r_mcangle_it5.758
r_mcangle_other5.757
r_dihedral_angle_1_deg5.626
r_scbond_it4.403
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.073
r_dihedral_angle_4_deg19.61
r_dihedral_angle_3_deg17.558
r_long_range_B_refined9.377
r_long_range_B_other9.376
r_scangle_other7.121
r_mcangle_it5.758
r_mcangle_other5.757
r_dihedral_angle_1_deg5.626
r_scbond_it4.403
r_scbond_other4.403
r_mcbond_other3.675
r_mcbond_it3.674
r_angle_refined_deg1.512
r_angle_other_deg0.961
r_chiral_restr0.072
r_bond_refined_d0.011
r_gen_planes_refined0.006
r_bond_other_d0.003
r_gen_planes_other0.003
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 Atoms7501
Nucleic Acid Atoms
Solvent Atoms4
Heterogen Atoms60

Software

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