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Structure of a 9-subunit archaeal exosome
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2BR2 PDB ENTRY 2BR2
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 = 135.49 α = 90 b = 135.49 β = 90 c = 135.49 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 1.6 50 100 0.1 11.7 7.9 106599
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 1.6 1.7 99.9 0.68 2.2 4.8
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-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2BR2 1.6 45.18 106599 2176 100 0.216 0.215 0.249 RANDOM 36.53
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 36.747 r_dihedral_angle_4_deg 19.874 r_dihedral_angle_3_deg 16.344 r_dihedral_angle_1_deg 7.626 r_scangle_it 3.353 r_scbond_it 2.329 r_mcangle_it 1.598 r_angle_refined_deg 1.549 r_mcbond_it 1.087 r_angle_other_deg 0.839
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.747 r_dihedral_angle_4_deg 19.874 r_dihedral_angle_3_deg 16.344 r_dihedral_angle_1_deg 7.626 r_scangle_it 3.353 r_scbond_it 2.329 r_mcangle_it 1.598 r_angle_refined_deg 1.549 r_mcbond_it 1.087 r_angle_other_deg 0.839 r_symmetry_vdw_refined 0.281 r_nbd_refined 0.201 r_symmetry_vdw_other 0.192 r_symmetry_hbond_refined 0.189 r_nbd_other 0.185 r_nbtor_refined 0.175 r_xyhbond_nbd_refined 0.164 r_chiral_restr 0.098 r_nbtor_other 0.089 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 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 5338 Nucleic Acid Atoms Solvent Atoms 398 Heterogen Atoms 24
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing