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Crystal structure of tetrameric RXRalpha-LBD complexed with antagonist danthron
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1G1U
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 277 100mM Tris, pH6.5, 10% PEG 4000, 5% glycerol , VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.53 51.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 115.026 α = 90 b = 99.924 β = 90 c = 47.201 γ = 90
Symmetry Space Group P 21 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 IMAGE PLATE RIGAKU RAXIS IV++ 2009-06-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.6 14.88 16495
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1G1U 2.6 14.88 16495 846 95.39 0.26518 0.26518 0.2656 0.31799 RANDOM 39.746
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 0.06 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.14 r_dihedral_angle_4_deg 20.293 r_dihedral_angle_3_deg 17.873 r_dihedral_angle_1_deg 5.542 r_scangle_it 1.507 r_angle_refined_deg 1.144 r_scbond_it 0.916 r_mcangle_it 0.795 r_mcbond_it 0.433 r_chiral_restr 0.076
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.14 r_dihedral_angle_4_deg 20.293 r_dihedral_angle_3_deg 17.873 r_dihedral_angle_1_deg 5.542 r_scangle_it 1.507 r_angle_refined_deg 1.144 r_scbond_it 0.916 r_mcangle_it 0.795 r_mcbond_it 0.433 r_chiral_restr 0.076 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3099 Nucleic Acid Atoms Solvent Atoms 84 Heterogen Atoms 18
Software Software Software Name Purpose CrystalClear data collection CNS refinement REFMAC refinement d*TREK data reduction d*TREK data scaling CNS phasing