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Crystal structure of the P. abyssi exosome RNase PH ring complexed with a single stranded 10-mer poly(A) RNA
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 2.61 52.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.555 α = 90 b = 93.555 β = 90 c = 125.951 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 2006-05-10 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 1.94 46.78 98.2 0.109 14.9 11 47831 46981 1 1 23.6
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) 1.94 2.06 90.1 0.627 3.5 9.2 6859
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 1.94 20 1 1 45299 44547 2374 98.34 0.19016 0.19016 0.18738 0.1857 0.24243 0.2379 RANDOM 29.413
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 38.956 r_dihedral_angle_3_deg 17.827 r_dihedral_angle_4_deg 17.121 r_dihedral_angle_1_deg 6.547 r_scangle_it 3.938 r_scbond_it 2.621 r_angle_refined_deg 2.065 r_mcangle_it 1.559 r_mcbond_it 1.101 r_nbtor_refined 0.328
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.956 r_dihedral_angle_3_deg 17.827 r_dihedral_angle_4_deg 17.121 r_dihedral_angle_1_deg 6.547 r_scangle_it 3.938 r_scbond_it 2.621 r_angle_refined_deg 2.065 r_mcangle_it 1.559 r_mcbond_it 1.101 r_nbtor_refined 0.328 r_symmetry_vdw_refined 0.244 r_nbd_refined 0.23 r_xyhbond_nbd_refined 0.195 r_symmetry_hbond_refined 0.191 r_chiral_restr 0.132 r_bond_refined_d 0.02 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3915 Nucleic Acid Atoms 154 Solvent Atoms 348 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MAR345dtb data collection XDS data reduction XDS data scaling MOLREP phasing