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Crystal structure of the P. abyssi exosome RNase PH ring complexed with UDP and GMP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2BA0 PDB ENTRY 2BA0
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 2.78 55.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.81 α = 90 b = 93.81 β = 90 c = 126.26 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 2006-04-01 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 2.14 43.98 99.3 0.172 11.3 14.8 36300 36060 1 1 28
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) 2.14 2.26 96 0.639 3.3 11.8 5542
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 2BA0 2.14 19.87 1 1 34174 33921 1783 99.26 0.19088 0.19088 0.18752 0.1862 0.25481 0.2466 RANDOM 32.856
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 -0.01 -0.02 0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.196 r_dihedral_angle_3_deg 20.369 r_dihedral_angle_4_deg 14.232 r_dihedral_angle_1_deg 9.836 r_scangle_it 4.074 r_scbond_it 2.787 r_angle_refined_deg 2.312 r_mcangle_it 1.593 r_mcbond_it 1.037 r_nbtor_refined 0.323
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.196 r_dihedral_angle_3_deg 20.369 r_dihedral_angle_4_deg 14.232 r_dihedral_angle_1_deg 9.836 r_scangle_it 4.074 r_scbond_it 2.787 r_angle_refined_deg 2.312 r_mcangle_it 1.593 r_mcbond_it 1.037 r_nbtor_refined 0.323 r_symmetry_vdw_refined 0.252 r_nbd_refined 0.243 r_xyhbond_nbd_refined 0.195 r_symmetry_hbond_refined 0.174 r_chiral_restr 0.164 r_bond_refined_d 0.023 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3913 Nucleic Acid Atoms Solvent Atoms 279 Heterogen Atoms 49
Software Software Software Name Purpose REFMAC refinement MAR345dtb data collection XDS data reduction XDS data scaling MOLREP phasing