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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
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, HANGING DROP 7.5 298 24% PEG 4000, 0.1M Tris, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.05 39.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.148 α = 90 b = 64.148 β = 90 c = 113.153 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 35.4 91.6 0.094 0.094 5.7 10.2 12643 11503 32.18
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) Redundancy Number Unique Reflections (All) 2.2 2.32 87.1 0.235 0.235 2.9 10.6 1549
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 35.4 11502 11502 561 90.98 0.198 0.198 0.196 0.2055 0.232 0.2427 RANDOM 29.102
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 -0.05 0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.635 r_dihedral_angle_4_deg 18.897 r_dihedral_angle_3_deg 14.428 r_dihedral_angle_1_deg 4.444 r_scangle_it 2.152 r_scbond_it 1.392 r_angle_refined_deg 1.199 r_mcangle_it 0.916 r_mcbond_it 0.535 r_nbtor_refined 0.299
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.635 r_dihedral_angle_4_deg 18.897 r_dihedral_angle_3_deg 14.428 r_dihedral_angle_1_deg 4.444 r_scangle_it 2.152 r_scbond_it 1.392 r_angle_refined_deg 1.199 r_mcangle_it 0.916 r_mcbond_it 0.535 r_nbtor_refined 0.299 r_symmetry_vdw_refined 0.205 r_nbd_refined 0.194 r_xyhbond_nbd_refined 0.132 r_chiral_restr 0.081 r_symmetry_hbond_refined 0.037 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 74 Heterogen Atoms 30
Software Software Software Name Purpose SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction DNA data collection MOSFLM data reduction MOLREP phasing