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Crystal Structure of the Retinoid X Receptor Ligand Binding Domain Bound to the Synthetic Agonist 3-[4-Hydroxy-3-(3,5,5,8,8-pentamethyl-5,6,7,8-tetrahydronaphthalen-2-yl)-phenyl]acrylic Acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1MVC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 298 20% PEG 4000, 0.1M TRIS, 1M AMMONIUM ACETATE, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.11 41.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.763 α = 90 b = 65.763 β = 90 c = 110.857 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 210 2007-07-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 0.934 ESRF ID14-1
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 31.53 99.9 0.077 0.077 6 17071 21.069
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 2.11 100 0.377 0.377 2 6.2 2433
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 1MVC 2 31.53 17071 17016 882 99.87 0.207 0.207 0.205 0.2069 0.241 0.2389 RANDOM 19.232
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] 0.62 0.62 -1.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.61 r_dihedral_angle_4_deg 21.69 r_dihedral_angle_3_deg 13.741 r_dihedral_angle_1_deg 4.609 r_scangle_it 2.406 r_scbond_it 1.544 r_angle_refined_deg 1.166 r_mcangle_it 1.069 r_mcbond_it 0.625 r_symmetry_hbond_refined 0.311
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.61 r_dihedral_angle_4_deg 21.69 r_dihedral_angle_3_deg 13.741 r_dihedral_angle_1_deg 4.609 r_scangle_it 2.406 r_scbond_it 1.544 r_angle_refined_deg 1.166 r_mcangle_it 1.069 r_mcbond_it 0.625 r_symmetry_hbond_refined 0.311 r_nbtor_refined 0.3 r_nbd_refined 0.194 r_symmetry_vdw_refined 0.185 r_xyhbond_nbd_refined 0.12 r_chiral_restr 0.085 r_bond_refined_d 0.01 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1752 Nucleic Acid Atoms Solvent Atoms 112 Heterogen Atoms 27
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction DNA data collection