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Crystal structure of RXRalphaLBD complexed with the agonist magnolol
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2P1T PDB ENTRY 2P1T
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 277 20% PEG3350, 100 mM Tris, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.13 42.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.95 α = 90 b = 65.83 β = 90 c = 110.29 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 MARMOSAIC 225 mm CCD 2010-05-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U SSRF BL17U
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 2.8 110.432 98.7 0.056 0.056 11.8 3.6 11863 11863 2 2
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) 1 2.85 2.9 99.7 0.381 0.381 2.7 3.6
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 (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 2P1T 2.8 56.6 11863 11760 575 99.81 0.25161 0.24937 0.2064 0.29279 0.204 RANDOM 46.513
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] -0.1 -0.12 0.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.857 r_dihedral_angle_4_deg 24.138 r_dihedral_angle_3_deg 17.761 r_dihedral_angle_1_deg 4.807 r_scangle_it 1.133 r_angle_refined_deg 1.069 r_scbond_it 0.679 r_mcangle_it 0.626 r_mcbond_it 0.351 r_nbtor_refined 0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.857 r_dihedral_angle_4_deg 24.138 r_dihedral_angle_3_deg 17.761 r_dihedral_angle_1_deg 4.807 r_scangle_it 1.133 r_angle_refined_deg 1.069 r_scbond_it 0.679 r_mcangle_it 0.626 r_mcbond_it 0.351 r_nbtor_refined 0.3 r_nbd_refined 0.204 r_symmetry_vdw_refined 0.19 r_xyhbond_nbd_refined 0.145 r_symmetry_hbond_refined 0.144 r_chiral_restr 0.076 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other 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 3557 Nucleic Acid Atoms Solvent Atoms 68 Heterogen Atoms 40
Software Software Software Name Purpose HKL-2000 data collection AMoRE phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling