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Structure of an Rrp6-RNA exosome complex bound to poly(A) RNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4IFD PDB ENTRIES 4IFD, 2NN6 AND 2HBL experimental model PDB 2NN6 PDB ENTRIES 4IFD, 2NN6 AND 2HBL experimental model PDB 2HBL PDB ENTRIES 4IFD, 2NN6 AND 2HBL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.7 291 7-11% PEG3350, 100 mM MES pH 6.7, 4-15% MPD, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.62 53.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 193.292 α = 90 b = 200.083 β = 90 c = 97.405 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 QUANTUM 315 2013-03-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 1.0750 NSLS X29A
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 3.3 50 97.7 0.061 15.5 5.2 56332 -1 -1 113.7
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 3.42 96.9 0.653 1.4 3.1
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-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT PDB ENTRIES 4IFD, 2NN6 AND 2HBL 3.3 48.426 1.37 56321 2855 97.73 0.2288 0.2268 0.2293 0.2649 0.264
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 8.524 f_angle_d 0.474 f_chiral_restr 0.032 f_bond_d 0.002 f_plane_restr 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 21445 Nucleic Acid Atoms 119 Solvent Atoms Heterogen Atoms 26
Software Software Software Name Purpose CBASS data collection PHENIX model building PHENIX refinement HKL-2000 data reduction SCALEPACK data scaling PHENIX phasing