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X-ray structure of benzisoxazole synthetic agonist bound to the LXR-alpha
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other In-house LXR-alpha complex
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 298 18% PEG MME 2000, 100mM (NH4)2SO4, 35mM Tris-HCl pH 7.8, 65mM Imidazole, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.43 49.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 123.051 α = 90 b = 123.051 β = 90 c = 91.636 γ = 90
Symmetry Space Group P 4 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 4 2005-11-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 0.9330 ESRF ID14-2
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 2.26 91.67 33516 33516
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.26 2.4 100
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 (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT In-house LXR-alpha complex 2.26 39.3 31554 1682 99.13 0.2581 0.25506 0.2585 0.3145 0.3142 RANDOM 37.443
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] 0.69 0.69 -1.39
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.389 r_dihedral_angle_3_deg 18.455 r_dihedral_angle_4_deg 17.909 r_dihedral_angle_1_deg 5.444 r_scangle_it 2.224 r_scbond_it 1.457 r_angle_refined_deg 1.412 r_mcangle_it 1.015 r_angle_other_deg 0.921 r_mcbond_it 0.912
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.389 r_dihedral_angle_3_deg 18.455 r_dihedral_angle_4_deg 17.909 r_dihedral_angle_1_deg 5.444 r_scangle_it 2.224 r_scbond_it 1.457 r_angle_refined_deg 1.412 r_mcangle_it 1.015 r_angle_other_deg 0.921 r_mcbond_it 0.912 r_symmetry_vdw_other 0.304 r_symmetry_hbond_refined 0.262 r_nbd_refined 0.209 r_nbd_other 0.186 r_nbtor_refined 0.186 r_xyhbond_nbd_refined 0.141 r_symmetry_vdw_refined 0.138 r_mcbond_other 0.114 r_nbtor_other 0.087 r_chiral_restr 0.073 r_bond_refined_d 0.013 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3931 Nucleic Acid Atoms Solvent Atoms 18 Heterogen Atoms 74
Software Software Software Name Purpose ADSC data collection MOLREP phasing REFMAC refinement CrystalClear data reduction CrystalClear data scaling