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Nuclear receptor DAF-12 from parasitic nematode Strongyloides stercoralis in complex with its physiological ligand dafachronic acid delta 7
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other ssDAF-12/delta4
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 2.9 57.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 120.946 α = 90 b = 120.946 β = 90 c = 40.757 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 2008-04-03 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 99.8 0.125 14.723 6.2 13572
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 0.669 2.58 6.2
Refinement Statistics Diffraction ID Structure Solution 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) Mean Isotropic B X-RAY DIFFRACTION ssDAF-12/delta4 2.4 39.59 13559 963 99.7 0.212 0.208 0.2091 0.255 0.2451 50.29
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] 0.42 0.21 0.42 -0.63
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.421 r_dihedral_angle_3_deg 16.965 r_dihedral_angle_4_deg 12.871 r_scangle_it 6.083 r_dihedral_angle_1_deg 4.297 r_angle_other_deg 3.873 r_scbond_it 3.76 r_mcangle_it 2.593 r_angle_refined_deg 1.897 r_mcbond_it 1.363
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.421 r_dihedral_angle_3_deg 16.965 r_dihedral_angle_4_deg 12.871 r_scangle_it 6.083 r_dihedral_angle_1_deg 4.297 r_angle_other_deg 3.873 r_scbond_it 3.76 r_mcangle_it 2.593 r_angle_refined_deg 1.897 r_mcbond_it 1.363 r_mcbond_other 0.292 r_chiral_restr 0.116 r_bond_refined_d 0.026 r_bond_other_d 0.007 r_gen_planes_refined 0.007 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 141 Heterogen Atoms 30
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction PHASER phasing