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Crystal structure of chicken MDA5 with 5'p 10-mer dsRNA and ADP-Mg2+ at 2.6 A resolution (orthorhombic form).
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 delta CARD-Q was mixed with 10 bp dsRNA in a 1:1 molar ratio and incubated for 30 minutes on ice. The complex was concentrated to around 10 mg/ml and 2 mM AMPPNP (adenosine 5 prime -(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 2.66 53.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.92 α = 90 b = 132.47 β = 90 c = 139.04 γ = 90
Symmetry Space Group P 21 21 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 PILATUS3 6M 2014-02-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.9763 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 98.2 0.096 10.3 5.06 57525
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 99.2 0.992 1.87 5.21
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 54624 2901 98.22 0.2784 0.27663 0.2781 0.31231 0.3097 RANDOM 65.634
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] -1.24 5.99 -4.75
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.861 r_dihedral_angle_3_deg 15.562 r_dihedral_angle_4_deg 12.63 r_dihedral_angle_1_deg 5.582 r_long_range_B_refined 2.277 r_long_range_B_other 2.23 r_angle_refined_deg 1.055 r_angle_other_deg 0.901 r_mcangle_it 0.592 r_mcangle_other 0.592
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.861 r_dihedral_angle_3_deg 15.562 r_dihedral_angle_4_deg 12.63 r_dihedral_angle_1_deg 5.582 r_long_range_B_refined 2.277 r_long_range_B_other 2.23 r_angle_refined_deg 1.055 r_angle_other_deg 0.901 r_mcangle_it 0.592 r_mcangle_other 0.592 r_scangle_other 0.477 r_mcbond_it 0.322 r_mcbond_other 0.322 r_scbond_it 0.259 r_scbond_other 0.259 r_chiral_restr 0.06 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 10771 Nucleic Acid Atoms 873 Solvent Atoms 168 Heterogen Atoms 58
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing