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Structure of duck RIG-I (delta CARDS) bound to 31-mer RNA mismatched hairpin with 5'pppG-C blunt end, mimicking the influenza B virus vRNA promoter (panhandle).
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 ADA 0.1 M
MgCl2 0.1M
PEG 6000 12 %
ZnCl2 0.1M
Crystal Properties Matthews coefficient Solvent content 2.35 47.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.641 α = 90 b = 100.072 β = 90 c = 192.287 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 2014-12-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.9792 ESRF ID23-1
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 1.488 96.144 81.3 0.098 0.999 13.8 8.7 112184
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 1.488 1.612 19.2 1.577 0.541 1.5 9.3
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 1.488 96.144 112184 5601 81.344 0.149 0.1472 0.1472 0.1914 0.1915 25.067
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] 1.323 -1.216 -0.108
RMS Deviations Key Refinement Restraint Deviation r_mcangle_it 32.867 r_mcangle_other 32.863 r_lrange_it 26.542 r_lrange_other 26.118 r_dihedral_angle_other_3_deg 26.008 r_mcbond_it 21.213 r_mcbond_other 21.212 r_dihedral_angle_6_deg 14.814 r_dihedral_angle_3_deg 11.742 r_scangle_it 10.861
RMS Deviations Key Refinement Restraint Deviation r_mcangle_it 32.867 r_mcangle_other 32.863 r_lrange_it 26.542 r_lrange_other 26.118 r_dihedral_angle_other_3_deg 26.008 r_mcbond_it 21.213 r_mcbond_other 21.212 r_dihedral_angle_6_deg 14.814 r_dihedral_angle_3_deg 11.742 r_scangle_it 10.861 r_scangle_other 10.86 r_scbond_it 6.055 r_scbond_other 6.054 r_dihedral_angle_1_deg 5.99 r_dihedral_angle_2_deg 5.715 r_rigid_bond_restr 2.615 r_angle_refined_deg 1.387 r_angle_other_deg 0.496 r_nbd_other 0.278 r_symmetry_nbd_refined 0.272 r_nbd_refined 0.231 r_symmetry_nbd_other 0.197 r_nbtor_refined 0.181 r_xyhbond_nbd_refined 0.165 r_dihedral_angle_other_2_deg 0.123 r_symmetry_xyhbond_nbd_refined 0.109 r_symmetry_xyhbond_nbd_other 0.083 r_symmetry_nbtor_other 0.074 r_chiral_restr 0.068 r_gen_planes_refined 0.006 r_bond_refined_d 0.005 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5411 Nucleic Acid Atoms 671 Solvent Atoms 599 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement XDS data reduction STARANISO data scaling MOLREP phasing