1UPW

Crystal structure of the human Liver X receptor beta ligand binding domain in complex with a synthetic agonist


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.5RESERVOIR: 25% MPD, 10% PEG4K, 100 MM HEPES PH 7.5, 10 MM D PROTEIN: 4-8 MG/ML IN 20 MM TRIS PH 8.0, 100 MM NACL, 10 MM
Crystal Properties
Matthews coefficientSolvent content
2.652.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 137.22α = 90
b = 43.276β = 90
c = 51.615γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHMIRRORS2002-10-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06SASLSX06SA

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
12.48989.90.1214.72.811049
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)
12.42.5392.40.3951.72.8

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1FCY2.4201050452787.60.250.295RANDOM13.18
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]
2.22-1.87-0.35
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.461
r_scangle_it3.243
r_scbond_it1.873
r_angle_refined_deg1.358
r_mcangle_it1.129
r_mcbond_it0.574
r_symmetry_vdw_refined0.261
r_nbd_refined0.218
r_symmetry_hbond_refined0.2
r_xyhbond_nbd_refined0.149
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.461
r_scangle_it3.243
r_scbond_it1.873
r_angle_refined_deg1.358
r_mcangle_it1.129
r_mcbond_it0.574
r_symmetry_vdw_refined0.261
r_nbd_refined0.218
r_symmetry_hbond_refined0.2
r_xyhbond_nbd_refined0.149
r_chiral_restr0.095
r_bond_refined_d0.012
r_gen_planes_refined0.004
r_bond_other_d
r_angle_other_deg
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_gen_planes_other
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
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 Atoms1875
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms31

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing