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Structure of C. thermophilum RNA exosome core
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model Modeller multi-template models built using structures of homolog proteins in silico model AlphaFold AF-G0S755-F1,AF-G0SC21-F1,AF-G0S1P1-F1,AF-G0SCD1-F1,AF-G0RZG4-F1,AF-P0CT46-F1,AF-G0RZX8-F1,AF-G0S9A0-F1,AF-G0SE33-F1 Rrp45,Rrp41,Rrp43,Rrp46,Rrp42,Mtr3,Rrp40,Rrp4,Csl4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 277 0.2M Ammonium Sulphate
0.1M Sodium Acetate pH 5.5
10% PEG MME 2000
Crystal Properties Matthews coefficient Solvent content 2.47 50.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.525 α = 90 b = 148.385 β = 90 c = 195.065 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 2016-03-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.99994 SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 48.9 99.57 0.984 5.01 13.5 29143 74.733
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.81 3.946 97.14 0.586 1.19 13.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 FREE R-VALUE 3.81 48.9 1.34 29114 1454 99.57 0.2456 0.2432 0.2432 0.2925 0.2929 Random selection 103.52
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 5.8183 f_angle_d 0.692 f_chiral_restr 0.0452 f_plane_restr 0.0044 f_bond_d 0.0042
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 17656 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose XDS data reduction XSCALE data scaling Coot model building PHENIX phasing PHENIX refinement ISOLDE model building