2P1T

Crystal structure of the ligand binding domain of the retinoid X receptor alpha in complex with 3-(2'-methoxy)-tetrahydronaphtyl cinnamic acid and a fragment of the coactivator TIF-2


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1MVCPDB entry 1mvc

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.529816% PEG 3350, 0.1M Tris, 1M ammonium acetate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal Properties
Matthews coefficientSolvent content
2.0439.63

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 64.15α = 90
b = 64.15β = 90
c = 112.692γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 4Toroidal mirror2007-02-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-2ESRFID14-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
11.837.599.90.0668.312.1225862253018.1
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.81.999.90.282.510.83222

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 1mvc1.8372258621434115299.920.1980.1980.1970.218RANDOM15.413
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]
0.240.24-0.47
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.37
r_dihedral_angle_4_deg22.469
r_dihedral_angle_3_deg12.881
r_dihedral_angle_1_deg4.67
r_scangle_it2.636
r_scbond_it1.699
r_angle_refined_deg1.147
r_mcangle_it1.038
r_mcbond_it0.599
r_symmetry_hbond_refined0.336
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.37
r_dihedral_angle_4_deg22.469
r_dihedral_angle_3_deg12.881
r_dihedral_angle_1_deg4.67
r_scangle_it2.636
r_scbond_it1.699
r_angle_refined_deg1.147
r_mcangle_it1.038
r_mcbond_it0.599
r_symmetry_hbond_refined0.336
r_nbtor_refined0.303
r_nbd_refined0.193
r_symmetry_vdw_refined0.182
r_xyhbond_nbd_refined0.096
r_chiral_restr0.091
r_bond_refined_d0.01
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1751
Nucleic Acid Atoms
Solvent Atoms112
Heterogen Atoms28

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
DNAdata collection
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing