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Unusual, dual endo- and exo-nuclease activity in the degradosome explained by crystal structure analysis of RNase J1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3BK1 PDB ENTRY 3BK1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8 0.2 M CACL2, 0.1 M TRIS.HCL, PH 8.0, 10 % (W/V) PEG 6000
Crystal Properties Matthews coefficient Solvent content 3.16 61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 177.823 α = 90 b = 209.43 β = 90 c = 74.106 γ = 90
Symmetry Space Group P 21 21 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 ADSC CCD 2010-01-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 Diamond I04
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 20 98.2 0.1 11.4 3.5 55920 -3 61.71
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 3.16 98.9 0.55 2.2 3.5
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT PDB ENTRY 3BK1 3 29.76 0.52 55828 2830 99.2 0.216 0.214 0.258 0.211
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] 19.6085 -12.9032 -6.7053
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 19.982 f_angle_d 1.324 f_chiral_restr 0.099 f_bond_d 0.01 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 16889 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 12
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHASER phasing