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Structure of duck RIG-I helicase domain bound to 19-mer dsRNA and ATP transition state analogue
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4A2P PDB ENTRY 4A2P
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 12 MG/ML, 1.2 TIMES MOLAR RATIO OF 19-MER DSRNA, 4 MM ADP, 2 MM ALF3 AND 0.1 M HEPES PH 7.5, 5% (V/V) ISO-PROPANOL AND 10% (W/V) PEG 4000.
Crystal Properties Matthews coefficient Solvent content 2.91 58.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 129.27 α = 90 b = 129.27 β = 90 c = 106.31 γ = 90
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 315r 2011-05-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 ESRF ID14-4
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 3.7 50 99.9 0.19 10.8 7.55 18825
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) 1 3.7 3.8 100 0.97 2.4 7.53
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 PDB ENTRY 4A2P 3.7 45.95 17885 940 99.93 0.19628 0.19278 0.1954 0.2627 0.2679 RANDOM 97.4
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] 0.77 0.77 -1.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.85 r_dihedral_angle_3_deg 21.087 r_dihedral_angle_4_deg 18.701 r_dihedral_angle_1_deg 7.14 r_angle_refined_deg 1.281 r_angle_other_deg 0.931 r_chiral_restr 0.071 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.85 r_dihedral_angle_3_deg 21.087 r_dihedral_angle_4_deg 18.701 r_dihedral_angle_1_deg 7.14 r_angle_refined_deg 1.281 r_angle_other_deg 0.931 r_chiral_restr 0.071 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_bond_other_d 0.002 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_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8348 Nucleic Acid Atoms 1562 Solvent Atoms Heterogen Atoms 64
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing