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Molecular basis of the phosphorothioation-sensing antiphage defence system DndBCDE-DndI
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other DndI-Se
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 277 4% PEG6000 and 100 mM MES monohydrate, pH 6.1
Crystal Properties Matthews coefficient Solvent content 2.81 56.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.379 α = 90 b = 135.078 β = 90 c = 225.078 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 ADSC QUANTUM 315r 2016-07-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U1 0.979 SSRF BL17U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) 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 50 99.8 0.169 18.6 13.3 31858
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3 3.11 100 1.335 0.372 0.838 13.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3 47.02 30146 1602 99.46 0.22745 0.22425 0.28553 0.2775 RANDOM 90.814
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] 5.9 -2.3 -3.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.088 r_dihedral_angle_3_deg 19.901 r_dihedral_angle_4_deg 18.512 r_long_range_B_refined 15.873 r_long_range_B_other 15.873 r_mcangle_it 11.869 r_mcangle_other 11.868 r_scangle_other 10.792 r_mcbond_it 7.794 r_mcbond_other 7.794
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.088 r_dihedral_angle_3_deg 19.901 r_dihedral_angle_4_deg 18.512 r_long_range_B_refined 15.873 r_long_range_B_other 15.873 r_mcangle_it 11.869 r_mcangle_other 11.868 r_scangle_other 10.792 r_mcbond_it 7.794 r_mcbond_other 7.794 r_scbond_it 7.054 r_scbond_other 7.054 r_dihedral_angle_1_deg 6.782 r_angle_other_deg 3.569 r_angle_refined_deg 1.308 r_chiral_restr 0.072 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 r_gen_planes_other 0.004 r_bond_other_d r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9769 Nucleic Acid Atoms Solvent Atoms 70 Heterogen Atoms 22
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling HKL-2000 data reduction REFMAC phasing