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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
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1MVC PDB entry 1mvc
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 298 14% PEG 10000, 0.1M Tris, 1M ammonium chloride, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.21 44.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.638 α = 90 b = 67.638 β = 90 c = 109.996 γ = 90
Symmetry Space Group P 43 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315 Toroidal mirror 2006-11-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 ESRF ID14-4
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) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.2 36.6 99.8 0.072 0.072 7.3 12.3 13627 13588 30
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) Redundancy Number Unique Reflections (All) 2.2 2.32 100 0.229 0.229 3.1 12.9 1938
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 1mvc 2.2 35 13585 13585 673 99.76 0.201 0.201 0.199 0.2131 0.251 0.2697 RANDOM 25.182
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] 0.73 0.73 -1.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.224 r_dihedral_angle_4_deg 20.366 r_dihedral_angle_3_deg 12.995 r_dihedral_angle_1_deg 4.786 r_scangle_it 2.515 r_scbond_it 1.518 r_angle_refined_deg 1.114 r_mcangle_it 0.947 r_mcbond_it 0.531 r_symmetry_hbond_refined 0.497
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.224 r_dihedral_angle_4_deg 20.366 r_dihedral_angle_3_deg 12.995 r_dihedral_angle_1_deg 4.786 r_scangle_it 2.515 r_scbond_it 1.518 r_angle_refined_deg 1.114 r_mcangle_it 0.947 r_mcbond_it 0.531 r_symmetry_hbond_refined 0.497 r_nbtor_refined 0.299 r_symmetry_vdw_refined 0.205 r_nbd_refined 0.187 r_xyhbond_nbd_refined 0.133 r_chiral_restr 0.082 r_bond_refined_d 0.009 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1751 Nucleic Acid Atoms Solvent Atoms 111 Heterogen Atoms 29
Software Software Software Name Purpose SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction DNA data collection MOSFLM data reduction MOLREP phasing