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Crystal structure of the P. abyssi exosome RNase PH ring complexed with ADP in double conformation
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2PNZ PDB ENTRY 2PNZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 291 0.1 M Bis-Tris, 45% MPD and 0.1 M LiCl, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291.0K
Crystal Properties Matthews coefficient Solvent content 2.83 56.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.2 α = 90 b = 94.2 β = 90 c = 127.7 γ = 120
Symmetry Space Group P 3 2 1
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 MAR CCD 165 mm mirrors 2006-05-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON LNLS BEAMLINE D03B-MX1 1.427 LNLS D03B-MX1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 44.23 97.5 0.093 16.5 9.7 29661 28933 1 1 41.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.3 2.44 89.6 0.451 3.7 8.4 4220
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 2PNZ 2.3 19.98 1 1 28026 26541 1433 94.7 0.19281 0.19281 0.19019 0.1859 0.24253 0.2352 RANDOM 38.197
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] -0.01 -0.01 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.861 r_dihedral_angle_4_deg 21.796 r_dihedral_angle_3_deg 20.148 r_dihedral_angle_1_deg 7.477 r_scangle_it 3.208 r_scbond_it 2.244 r_angle_refined_deg 2.156 r_mcangle_it 1.148 r_mcbond_it 0.751 r_nbtor_refined 0.316
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.861 r_dihedral_angle_4_deg 21.796 r_dihedral_angle_3_deg 20.148 r_dihedral_angle_1_deg 7.477 r_scangle_it 3.208 r_scbond_it 2.244 r_angle_refined_deg 2.156 r_mcangle_it 1.148 r_mcbond_it 0.751 r_nbtor_refined 0.316 r_symmetry_vdw_refined 0.25 r_nbd_refined 0.241 r_symmetry_hbond_refined 0.222 r_xyhbond_nbd_refined 0.213 r_chiral_restr 0.13 r_bond_refined_d 0.021 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3900 Nucleic Acid Atoms Solvent Atoms 175 Heterogen Atoms 54
Software Software Software Name Purpose REFMAC refinement MAR345dtb data collection XDS data reduction XDS data scaling MOLREP phasing