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Structure of duck RIG-I (delta CARDs) bound to 31-mer RNA mismatched hairpin with 5'ppA-U blunt end mimicking the influenza B virus vRNA promoter (panhandle) and to ADP.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4A36
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 288 Na-citrate pH 5.5
PEG 3000 22 %
NDSB 201 0,1M
Crystal Properties Matthews coefficient Solvent content 2.33 47.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.883 α = 90 b = 100.026 β = 90 c = 190.128 γ = 90
Symmetry Space Group C 2 2 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 PIXEL DECTRIS PILATUS 6M 2014-10-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.9791 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 1.704 95.064 77 0.109 0.922 8.6 16.9 70381
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.704 1.859 1.024 0.566 1.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.704 95.064 70380 3472 76.99 0.187 0.1853 0.1929 0.2252 0.2289 32.057
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] 0.078 0.02 -0.097
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_other_3_deg 20.849 r_dihedral_angle_6_deg 15.409 r_dihedral_angle_3_deg 13.599 r_lrange_it 7.621 r_lrange_other 7.602 r_dihedral_angle_2_deg 7.164 r_dihedral_angle_1_deg 6.452 r_scangle_it 5.583 r_scangle_other 5.582 r_mcangle_it 4.046
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_other_3_deg 20.849 r_dihedral_angle_6_deg 15.409 r_dihedral_angle_3_deg 13.599 r_lrange_it 7.621 r_lrange_other 7.602 r_dihedral_angle_2_deg 7.164 r_dihedral_angle_1_deg 6.452 r_scangle_it 5.583 r_scangle_other 5.582 r_mcangle_it 4.046 r_mcangle_other 4.046 r_scbond_it 3.558 r_scbond_other 3.558 r_mcbond_it 2.615 r_mcbond_other 2.613 r_angle_refined_deg 1.593 r_angle_other_deg 0.541 r_symmetry_nbd_refined 0.309 r_dihedral_angle_other_2_deg 0.287 r_nbd_other 0.257 r_nbd_refined 0.226 r_xyhbond_nbd_refined 0.199 r_symmetry_nbd_other 0.195 r_nbtor_refined 0.181 r_symmetry_xyhbond_nbd_refined 0.17 r_symmetry_nbtor_other 0.077 r_chiral_restr 0.076 r_symmetry_xyhbond_nbd_other 0.016 r_gen_planes_refined 0.007 r_bond_refined_d 0.006 r_metal_ion_refined 0.006 r_symmetry_metal_ion_refined 0.006 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5435 Nucleic Acid Atoms 557 Solvent Atoms 333 Heterogen Atoms 42
Software Software Software Name Purpose REFMAC refinement XDS data reduction STARANISO data scaling MOLREP phasing