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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 1.99 38.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.079 α = 90 b = 64.079 β = 90 c = 110.389 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 2007-10-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 1.00 ESRF ID29
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 3 50 99.9 0.102 0.102 33.776 12.3 5032 5032 57.611
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) 3 3.11 100 0.333 12.6 481
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-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION THROUGHOUT PDB ENTRY 1MZN 3 10 4831 226 100 0.21 0.21 0.206 0.278 RANDOM 41.876
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] 0.66 0.66 -1.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.847 r_dihedral_angle_4_deg 22.165 r_dihedral_angle_3_deg 14.445 r_dihedral_angle_1_deg 3.734 r_angle_refined_deg 1.023 r_scangle_it 0.677 r_mcangle_it 0.422 r_scbond_it 0.399 r_nbtor_refined 0.291 r_mcbond_it 0.228
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.847 r_dihedral_angle_4_deg 22.165 r_dihedral_angle_3_deg 14.445 r_dihedral_angle_1_deg 3.734 r_angle_refined_deg 1.023 r_scangle_it 0.677 r_mcangle_it 0.422 r_scbond_it 0.399 r_nbtor_refined 0.291 r_mcbond_it 0.228 r_nbd_refined 0.172 r_symmetry_vdw_refined 0.169 r_xyhbond_nbd_refined 0.109 r_symmetry_hbond_refined 0.107 r_chiral_restr 0.059 r_bond_refined_d 0.006 r_gen_planes_refined 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1778 Nucleic Acid Atoms Solvent Atoms 21 Heterogen Atoms 27
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