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Structure of a 12-subunit nuclear exosome complex bound to structured RNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4IFD 4IFD, 2HBJ experimental model PDB 2HBJ 4IFD, 2HBJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 283 7%(w/v) PEG 8000, 0.1M MES pH 6.5, 0.15M NaCl, 5%(v/v) Glycerol, 283K or 292K
Crystal Properties Matthews coefficient Solvent content 2.85 56.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 106.15 α = 90 b = 177.39 β = 90 c = 299.9 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 PILATUS 6M 2014-03-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 1.2398 APS 17-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 3.81 57.887 80.8 0.163 0.175 4.83 5.6 45806 -3 159.59
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.81 4.2 38 0.843 1.081 0.69 1.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation 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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4IFD, 2HBJ 3.812 57.887 1.33 45723 2286 81.45 0.2949 0.2947 0.2965 0.2996 0.3028 Random selection 270.9274
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 10.17 f_angle_d 0.704 f_chiral_restr 0.045 f_plane_restr 0.005 f_bond_d 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 27238 Nucleic Acid Atoms 557 Solvent Atoms Heterogen Atoms 1
Software Software Software Name Purpose XDS data reduction XSCALE data scaling PHASER phasing PHENIX refinement Coot model building PDB_EXTRACT data extraction