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RNase PH core of the archaeal exosome in complex with ADP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2BR3 PDB ENTRY 2BR3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 50 MM MES, 2.4 M SODIUM MALONATE, PH 7.0
Crystal Properties Matthews coefficient Solvent content 3.4 63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 206.2 α = 90 b = 214 β = 90 c = 432.5 γ = 90
Symmetry Space Group C 2 2 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 CCD MARRESEARCH 2005-04-17 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 3.3 100 93.8 0.18 8.1 4.4 129777 -3
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 3.3 3.5 95.3 0.75 2.4 4.3
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 2BR3 3.3 93.25 129777 4015 100 0.275 0.274 0.2652 0.295 0.2829 RANDOM 54.17
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] -0.02 0.05 -0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.173 r_dihedral_angle_4_deg 18.94 r_dihedral_angle_3_deg 18.688 r_dihedral_angle_1_deg 5.919 r_scangle_it 1.49 r_angle_refined_deg 1.224 r_scbond_it 0.831 r_mcangle_it 0.652 r_mcbond_it 0.376 r_nbtor_refined 0.306
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.173 r_dihedral_angle_4_deg 18.94 r_dihedral_angle_3_deg 18.688 r_dihedral_angle_1_deg 5.919 r_scangle_it 1.49 r_angle_refined_deg 1.224 r_scbond_it 0.831 r_mcangle_it 0.652 r_mcbond_it 0.376 r_nbtor_refined 0.306 r_symmetry_hbond_refined 0.279 r_symmetry_vdw_refined 0.234 r_nbd_refined 0.206 r_xyhbond_nbd_refined 0.148 r_chiral_restr 0.075 r_bond_refined_d 0.01 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_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 45538 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 276
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling