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Structure of a 9-subunit archaeal exosome bound to Mn ions
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 = 133.64 α = 90 b = 133.64 β = 90 c = 133.64 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 2.4 50 99.5 0.06 17.9 5.5 29796
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 2.4 2.5 97.6 0.44 2.7 2.9
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 2.4 44.54 29796 1568 100 0.201 0.198 0.2518 0.258 0.3035 RANDOM 45.36
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 36.37 r_dihedral_angle_4_deg 18.256 r_dihedral_angle_3_deg 17.914 r_dihedral_angle_1_deg 6.517 r_scangle_it 1.621 r_angle_refined_deg 1.262 r_scbond_it 1.056 r_angle_other_deg 0.745 r_mcangle_it 0.699 r_mcbond_it 0.461
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.37 r_dihedral_angle_4_deg 18.256 r_dihedral_angle_3_deg 17.914 r_dihedral_angle_1_deg 6.517 r_scangle_it 1.621 r_angle_refined_deg 1.262 r_scbond_it 1.056 r_angle_other_deg 0.745 r_mcangle_it 0.699 r_mcbond_it 0.461 r_nbd_refined 0.188 r_symmetry_vdw_refined 0.188 r_nbd_other 0.18 r_nbtor_refined 0.17 r_xyhbond_nbd_refined 0.169 r_symmetry_vdw_other 0.165 r_symmetry_hbond_refined 0.154 r_nbtor_other 0.086 r_chiral_restr 0.07 r_bond_refined_d 0.009 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_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 5239 Nucleic Acid Atoms Solvent Atoms 168 Heterogen Atoms 19
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing