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Rhs2-CT endonuclease toxin in complex with cognate immunity protein RhsI2 and EF-Tu
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1EFC experimental model Other Solved and refined by X-ray crystallography in this study (not previously deposited) in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 296 0.2 uL of 18 mg/mL Rhs2-ct-RhsI2-EF-Tu (in 20 mM Tris-HCl pH 7.5, 250 mM NaCl, 2 mM MgCl2, 2 mM GDP and 0.5 mM TCEP) mixed with 0.2 uL of reservoir solution (0.2 M ammonium actetate, 0.1 M HEPES pH 7.5 and 25% PEG3350). Cryoprotected with Paratone N
Crystal Properties Matthews coefficient Solvent content 2.59 52.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.598 α = 90 b = 110.569 β = 102.392 c = 113.863 γ = 90
Symmetry Space Group P 1 21 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 PIXEL DECTRIS EIGER2 XE 16M 2021-11-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9763 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 2.45 60.236 100 0.151 0.988 6 6.7 54856
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 2.45 2.52 1.721 1.134 0.443
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.45 60.236 54781 2724 99.896 0.273 0.2704 0.2736 0.3138 0.3163 57.338
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] -3.327 0.085 -0.509 3.464
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.676 r_dihedral_angle_4_deg 20.108 r_dihedral_angle_3_deg 15.661 r_lrange_it 9.916 r_lrange_other 9.916 r_dihedral_angle_1_deg 6.273 r_mcangle_it 5.5 r_mcangle_other 5.499 r_scangle_it 5.464 r_scangle_other 5.464
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.676 r_dihedral_angle_4_deg 20.108 r_dihedral_angle_3_deg 15.661 r_lrange_it 9.916 r_lrange_other 9.916 r_dihedral_angle_1_deg 6.273 r_mcangle_it 5.5 r_mcangle_other 5.499 r_scangle_it 5.464 r_scangle_other 5.464 r_mcbond_it 3.595 r_mcbond_other 3.594 r_scbond_it 3.455 r_scbond_other 3.455 r_angle_other_deg 1.381 r_angle_refined_deg 1.265 r_nbd_other 0.255 r_symmetry_nbd_refined 0.223 r_symmetry_nbd_other 0.201 r_nbd_refined 0.187 r_xyhbond_nbd_refined 0.165 r_nbtor_refined 0.16 r_metal_ion_refined 0.141 r_ncsr_local_group_2 0.086 r_ncsr_local_group_3 0.083 r_symmetry_nbtor_other 0.081 r_symmetry_xyhbond_nbd_refined 0.074 r_ncsr_local_group_1 0.069 r_chiral_restr 0.057 r_symmetry_xyhbond_nbd_other 0.011 r_bond_refined_d 0.006 r_gen_planes_refined 0.005 r_bond_other_d 0.003 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10265 Nucleic Acid Atoms Solvent Atoms 146 Heterogen Atoms 76
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing