2P1U

Crystal structure of the ligand binding domain of the retinoid X receptor alpha in complex with 3-(2'-ethoxy)-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, SITTING DROP8.529814% PEG 10000, 0.1M Tris, 1M ammonium chloride, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.2144.37

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 67.638α = 90
b = 67.638β = 90
c = 109.996γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315Toroidal mirror2006-11-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-4ESRFID14-4

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
12.236.699.80.0720.0727.312.3136271358830
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.22.321000.2290.2293.112.91938

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 1mvc2.235135851358567399.760.2010.2010.1990.251RANDOM25.182
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]
0.730.73-1.45
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.224
r_dihedral_angle_4_deg20.366
r_dihedral_angle_3_deg12.995
r_dihedral_angle_1_deg4.786
r_scangle_it2.515
r_scbond_it1.518
r_angle_refined_deg1.114
r_mcangle_it0.947
r_mcbond_it0.531
r_symmetry_hbond_refined0.497
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.224
r_dihedral_angle_4_deg20.366
r_dihedral_angle_3_deg12.995
r_dihedral_angle_1_deg4.786
r_scangle_it2.515
r_scbond_it1.518
r_angle_refined_deg1.114
r_mcangle_it0.947
r_mcbond_it0.531
r_symmetry_hbond_refined0.497
r_nbtor_refined0.299
r_symmetry_vdw_refined0.205
r_nbd_refined0.187
r_xyhbond_nbd_refined0.133
r_chiral_restr0.082
r_bond_refined_d0.009
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1751
Nucleic Acid Atoms
Solvent Atoms111
Heterogen Atoms29

Software

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