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Crystal structure of the human RXR alpha ligand binding domain bound to a synthetic agonist compound and a coactivator peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1MZN PDB ENTRY 1MZN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 290 10mM Tris-HCl, 250mM NaCl, 5mM DTT, 50mM calcium acetate, 18% PEG3350, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal Properties Matthews coefficient Solvent content 2.12 41.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.975 α = 90 b = 66.85 β = 90 c = 110.793 γ = 90
Symmetry Space Group P 21 21 21
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 4 2007-09-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 0.933 ESRF ID14-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.9 50 99.7 0.081 36.767 7 11166 11166 65.993
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.9 3 100 0.317 7.2 1094
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 Selection Details Mean Isotropic B X-RAY DIFFRACTION THROUGHOUT PDB ENTRY 1MZN 2.9 10 10834 512 99.58 0.221 0.221 0.217 0.2101 0.289 RANDOM 48.367
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] 5.37 -1.6 -3.77
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.676 r_dihedral_angle_4_deg 23.301 r_dihedral_angle_3_deg 15.385 r_dihedral_angle_1_deg 4.309 r_angle_refined_deg 1.043 r_scangle_it 0.88 r_scbond_it 0.552 r_mcangle_it 0.502 r_nbtor_refined 0.293 r_mcbond_it 0.268
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.676 r_dihedral_angle_4_deg 23.301 r_dihedral_angle_3_deg 15.385 r_dihedral_angle_1_deg 4.309 r_angle_refined_deg 1.043 r_scangle_it 0.88 r_scbond_it 0.552 r_mcangle_it 0.502 r_nbtor_refined 0.293 r_mcbond_it 0.268 r_nbd_refined 0.178 r_symmetry_vdw_refined 0.166 r_xyhbond_nbd_refined 0.128 r_chiral_restr 0.069 r_symmetry_hbond_refined 0.049 r_bond_refined_d 0.006 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3601 Nucleic Acid Atoms Solvent Atoms 26 Heterogen Atoms 54
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling AMoRE phasing