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Structure of an eleven component nuclear RNA exosome complex bound to RNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4OO1 4OO1, 2WP8 experimental model PDB 2WP8 4OO1, 2WP8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 277 100 mM sodium citrate pH 5.25, 7 mM sodium MES pH 6.5, 6.7% PEG 3350, 175 mM (NH4)2SO4, 0.5 mM MgCl2, 40 mM TRIS-Cl pH 8.0, 200 mM NaCl, 2 mM TCEP-HCl
Crystal Properties Matthews coefficient Solvent content 3.42 64.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 140.701 α = 90 b = 212.257 β = 90 c = 218.231 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-F 2015-07-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.9795 APS 24-ID-C
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 3.1 106.13 98.8 0.116 14.3 3.6 116037 66.2
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 3.1 3.21 97 0.534 2.8 3
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 4OO1, 2WP8 3.1 106.13 1 116007 5764 97.6 0.203 0.201 0.2021 0.249 0.2496 Random
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 11.905 f_angle_d 0.425 f_chiral_restr 0.04 f_plane_restr 0.003 f_bond_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 29376 Nucleic Acid Atoms 502 Solvent Atoms 280 Heterogen Atoms 93
Software Software Software Name Purpose PHENIX refinement SCALEPACK data scaling PHASER phasing PDB_EXTRACT data extraction Coot model building HKL-2000 data reduction