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Structure of the N-terminal deletion of yeast exosome component Rrp40
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 20% (W/V) PEG 3350,200 MM NA2SO4
Crystal Properties Matthews coefficient Solvent content 3.6 65.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 153.51 α = 90 b = 153.51 β = 90 c = 153.51 γ = 90
Symmetry Space Group I 41 3 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 MARRESEARCH 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 2.2 50 99 0.12 34 45 15115
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 2.2 97.2 0.59 8.9 36
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 SAD THROUGHOUT 2.2 14.91 15115 796 100 0.19 0.189 0.26 0.206 0.2657 RANDOM 42.22
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 39.609 r_dihedral_angle_4_deg 14.937 r_dihedral_angle_3_deg 13.191 r_dihedral_angle_1_deg 5.732 r_scangle_it 1.482 r_scbond_it 1.005 r_angle_refined_deg 0.997 r_mcangle_it 0.714 r_angle_other_deg 0.71 r_mcbond_it 0.654
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.609 r_dihedral_angle_4_deg 14.937 r_dihedral_angle_3_deg 13.191 r_dihedral_angle_1_deg 5.732 r_scangle_it 1.482 r_scbond_it 1.005 r_angle_refined_deg 0.997 r_mcangle_it 0.714 r_angle_other_deg 0.71 r_mcbond_it 0.654 r_symmetry_vdw_other 0.228 r_symmetry_vdw_refined 0.192 r_nbd_refined 0.183 r_nbtor_refined 0.174 r_nbd_other 0.157 r_symmetry_hbond_refined 0.132 r_xyhbond_nbd_refined 0.131 r_nbtor_other 0.076 r_mcbond_other 0.066 r_chiral_restr 0.06 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 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_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 1338 Nucleic Acid Atoms Solvent Atoms 96 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement SHELX phasing