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Structure of a 9-subunit archaeal exosome bound to RNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2JE6 PDB ENTRY 2JE6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8 40% PEG 400 50 MM TRIS-HCL PH 8.0
Crystal Properties Matthews coefficient Solvent content 2.3 46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 135.85 α = 90 b = 135.85 β = 90 c = 135.85 γ = 90
Symmetry Space Group P 21 3
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 MARRESEARCH 2006-07-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA SLS X06SA
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 2.3 50 95.9 0.08 14.8 6.2 34014
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 2.3 2.4 66.5 0.67 2.8 6.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 PDB ENTRY 2JE6 2.33 42.95 34014 1790 100 0.207 0.205 0.2695 0.243 0.2855 RANDOM 51.67
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 r_dihedral_angle_2_deg 36.78 r_dihedral_angle_4_deg 20.869 r_dihedral_angle_3_deg 17.846 r_dihedral_angle_1_deg 7.007 r_scangle_it 2.25 r_angle_refined_deg 1.423 r_scbond_it 1.344 r_mcangle_it 0.909 r_angle_other_deg 0.792 r_mcbond_it 0.549
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.78 r_dihedral_angle_4_deg 20.869 r_dihedral_angle_3_deg 17.846 r_dihedral_angle_1_deg 7.007 r_scangle_it 2.25 r_angle_refined_deg 1.423 r_scbond_it 1.344 r_mcangle_it 0.909 r_angle_other_deg 0.792 r_mcbond_it 0.549 r_nbd_refined 0.207 r_nbd_other 0.181 r_nbtor_refined 0.178 r_xyhbond_nbd_refined 0.17 r_symmetry_vdw_other 0.164 r_symmetry_hbond_refined 0.155 r_symmetry_vdw_refined 0.138 r_nbtor_other 0.086 r_chiral_restr 0.076 r_bond_refined_d 0.012 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5304 Nucleic Acid Atoms 112 Solvent Atoms 122 Heterogen Atoms 16
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing