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Crystal structure of chicken MDA5 with 5'p 10-mer dsRNA and ADP-Mg2+ at 2.6 A resolution (monoclinic form, twinned).
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4GL2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 Directly after size exclusion chromatography chMDA5 deltaCARD-Q was mixed with 10 bp dsRNA in a 1:1 molar ratio and incubated for 30 minutes on ice. The complex was concentrated using an Amicon Ultra concentrator to around 10 mg/ml and 2 mM AMPPNP (adenosine 5prime-(beta,gamma-imido)triphosphate lithium salt hydrate) was added. Sample and reservoir buffer (0.025 M Bis-Tris pH 6.5, 0.075 M succinic acid pH 7.0, 12-14% PEG 3350, 2% sucrose) were mixed in a 2:1 ratio. Three hours after setup, cover glasses with drops were transferred from a reservoir containing 12-14% PEG 3350 to one containing 8% PEG 3350. Crystals grew in one week at 20 C and were harvested in cryo-protectant solution (0.025 M Bis-Tris pH 6.5, 0.075 M succinic acid pH 7.0, 25% 3350, 10% ethylene glycol) before flash freezing with liquid nitrogen.
Crystal Properties Matthews coefficient Solvent content 2.69 54.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.16 α = 90 b = 138.7 β = 109.47 c = 100.43 γ = 90
Symmetry Space Group P 1 21 1
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 PILATUS3 6M 2014-03-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.9724 ESRF ID29
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 2.6 50 99.3 0.096 9.83 3.52 55300
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 2.6 2.69 99.6 0.896 1.73 3.63
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 4GL2 2.6 50 52489 2811 99.39 0.27205 0.27111 0.2841 0.28962 0.3062 RANDOM 57.742
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] -0.55 0.06 0.31 0.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.672 r_dihedral_angle_3_deg 15.799 r_dihedral_angle_4_deg 13.602 r_dihedral_angle_1_deg 5.959 r_long_range_B_refined 4.583 r_long_range_B_other 4.583 r_mcangle_it 3.124 r_mcangle_other 3.124 r_scangle_other 2.622 r_mcbond_it 1.796
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.672 r_dihedral_angle_3_deg 15.799 r_dihedral_angle_4_deg 13.602 r_dihedral_angle_1_deg 5.959 r_long_range_B_refined 4.583 r_long_range_B_other 4.583 r_mcangle_it 3.124 r_mcangle_other 3.124 r_scangle_other 2.622 r_mcbond_it 1.796 r_mcbond_other 1.795 r_scbond_it 1.516 r_scbond_other 1.516 r_angle_refined_deg 1.113 r_angle_other_deg 0.912 r_chiral_restr 0.065 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10847 Nucleic Acid Atoms 854 Solvent Atoms Heterogen Atoms 58
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing