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Crystal structure of human DECH-box RNA Helicase MDA5 (Melanoma differentiation-associated protein 5), DECH-domain
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 298 1.2M Sodium citrate, 0.1M Tris-HCl, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.9 57.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.83 α = 90 b = 72.83 β = 90 c = 182.78 γ = 120
Symmetry Space Group P 65 2 2
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 MARMOSAIC 225 mm CCD Mirrors 2007-06-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 1.0000 BESSY 14.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.6 20 99.7 0.047 0.033 37.7 16 38652 38652
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.7 100 0.343 0.196 7.4 10 6278
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD THROUGHOUT 1.6 19.97 36717 36717 1933 100 0.18057 0.18057 0.17936 0.20371 0.2518 RANDOM 16.086
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] 0.18 0.09 0.18 -0.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.57 r_dihedral_angle_4_deg 16.808 r_dihedral_angle_3_deg 13.766 r_dihedral_angle_1_deg 5.736 r_scangle_it 4.672 r_scbond_it 2.781 r_mcangle_it 1.847 r_angle_refined_deg 1.536 r_mcbond_it 0.988 r_angle_other_deg 0.908
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.57 r_dihedral_angle_4_deg 16.808 r_dihedral_angle_3_deg 13.766 r_dihedral_angle_1_deg 5.736 r_scangle_it 4.672 r_scbond_it 2.781 r_mcangle_it 1.847 r_angle_refined_deg 1.536 r_mcbond_it 0.988 r_angle_other_deg 0.908 r_symmetry_vdw_other 0.263 r_mcbond_other 0.263 r_symmetry_vdw_refined 0.238 r_nbd_refined 0.22 r_xyhbond_nbd_refined 0.191 r_nbd_other 0.185 r_nbtor_refined 0.176 r_symmetry_hbond_refined 0.116 r_chiral_restr 0.092 r_nbtor_other 0.086 r_bond_refined_d 0.015 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1441 Nucleic Acid Atoms Solvent Atoms 174 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement MAR345 data collection XDS data reduction XSCALE data scaling SHELX phasing