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Nuclear receptor DAF-12 from parasitic nematode Strongyloides stercoralis in complex with its physiological ligand dafachronic acid delta 4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 PEG 8000, ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.8 56.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 118.947 α = 90 b = 118.947 β = 90 c = 40.225 γ = 120
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 300 mm CCD mirrors 2008-08-03 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 1.0 APS 23-ID-B
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 2.4 50 99.964 0.172 23.915 14.8 13012
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) 2.4 2.49 100 0.655 7.34 14.1
Refinement Statistics Diffraction ID Structure Solution Method 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT 2.4 30 12999 910 100 0.195 0.192 0.1962 0.232 0.2271 22.78
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] 0.39 0.19 0.39 -0.58
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.765 r_dihedral_angle_4_deg 17.199 r_dihedral_angle_3_deg 16.589 r_scangle_it 5.512 r_dihedral_angle_1_deg 3.972 r_angle_other_deg 3.835 r_scbond_it 3.343 r_mcangle_it 2.404 r_angle_refined_deg 1.686 r_mcbond_it 1.216
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.765 r_dihedral_angle_4_deg 17.199 r_dihedral_angle_3_deg 16.589 r_scangle_it 5.512 r_dihedral_angle_1_deg 3.972 r_angle_other_deg 3.835 r_scbond_it 3.343 r_mcangle_it 2.404 r_angle_refined_deg 1.686 r_mcbond_it 1.216 r_mcbond_other 0.257 r_chiral_restr 0.095 r_bond_refined_d 0.025 r_gen_planes_refined 0.007 r_bond_other_d 0.006 r_gen_planes_other 0.001 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2022 Nucleic Acid Atoms Solvent Atoms 168 Heterogen Atoms 30
Software Software Software Name Purpose PHASER phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction SCALEPACK data scaling