3NSQ

Crystal structure of tetrameric RXRalpha-LBD complexed with antagonist danthron


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1G1U 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.5277100mM Tris, pH6.5, 10% PEG 4000, 5% glycerol , VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.5351.29

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 115.026α = 90
b = 99.924β = 90
c = 47.201γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-rayIMAGE PLATERIGAKU RAXIS IV++2009-06-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU1.5418

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
12.614.8816495

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 REPLACEMENTTHROUGHOUT1G1U2.614.881649584695.390.265180.265180.31799RANDOM39.746
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]
-0.050.06-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.14
r_dihedral_angle_4_deg20.293
r_dihedral_angle_3_deg17.873
r_dihedral_angle_1_deg5.542
r_scangle_it1.507
r_angle_refined_deg1.144
r_scbond_it0.916
r_mcangle_it0.795
r_mcbond_it0.433
r_chiral_restr0.076
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.14
r_dihedral_angle_4_deg20.293
r_dihedral_angle_3_deg17.873
r_dihedral_angle_1_deg5.542
r_scangle_it1.507
r_angle_refined_deg1.144
r_scbond_it0.916
r_mcangle_it0.795
r_mcbond_it0.433
r_chiral_restr0.076
r_bond_refined_d0.008
r_gen_planes_refined0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3099
Nucleic Acid Atoms
Solvent Atoms84
Heterogen Atoms18

Software

Software
Software NamePurpose
CrystalCleardata collection
CNSrefinement
REFMACrefinement
d*TREKdata reduction
d*TREKdata scaling
CNSphasing