2P1V

Crystal structure of the ligand binding domain of the retinoid X receptor alpha in complex with 3-(2'-propoxy)-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 DROP7.529824% PEG 4000, 0.1M Tris, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.0539.88

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 64.148α = 90
b = 64.148β = 90
c = 113.153γ = 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
12.235.491.60.0940.0945.710.2126431150332.18
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)
2.22.3287.10.2350.2352.910.61549

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 1mvc2.235.4115021150256190.980.1980.1980.1960.232RANDOM29.102
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]
-0.05-0.050.09
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.635
r_dihedral_angle_4_deg18.897
r_dihedral_angle_3_deg14.428
r_dihedral_angle_1_deg4.444
r_scangle_it2.152
r_scbond_it1.392
r_angle_refined_deg1.199
r_mcangle_it0.916
r_mcbond_it0.535
r_nbtor_refined0.299
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.635
r_dihedral_angle_4_deg18.897
r_dihedral_angle_3_deg14.428
r_dihedral_angle_1_deg4.444
r_scangle_it2.152
r_scbond_it1.392
r_angle_refined_deg1.199
r_mcangle_it0.916
r_mcbond_it0.535
r_nbtor_refined0.299
r_symmetry_vdw_refined0.205
r_nbd_refined0.194
r_xyhbond_nbd_refined0.132
r_chiral_restr0.081
r_symmetry_hbond_refined0.037
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 Atoms74
Heterogen Atoms30

Software

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