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A viral SAVED protein with ring nuclease activity subverts type III CRISPR defence
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 10.5 293 1.2M sodium phosphate
0.8M potassium phosphate
0.2M lithium phosphate
0.1M CAPS pH 10.5
Crystal Properties Matthews coefficient Solvent content 3.71 66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 110.614 α = 90 b = 110.614 β = 90 c = 113.027 γ = 120
Symmetry Space Group P 31 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 PIXEL DECTRIS EIGER2 X 16M 2024-02-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9537 Diamond I04
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 1.79 95.93 100 0.115 1 17.4 38.9 75593
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.79 1.82 100 4.572 0.345
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION AB INITIO PHASING THROUGHOUT 1.79 95.794 75149 1997 99.467 0.166 0.1649 0.1783 0.2071 0.2167 RANDOM 41.399
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] -0.769 -0.384 -0.769 2.493
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 27.873 r_lrange_other 27.827 r_scangle_it 24.653 r_scangle_other 24.607 r_mcangle_other 19.333 r_mcangle_it 19.328 r_scbond_it 18.196 r_scbond_other 18.151 r_mcbond_it 14.596 r_mcbond_other 14.587
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 27.873 r_lrange_other 27.827 r_scangle_it 24.653 r_scangle_other 24.607 r_mcangle_other 19.333 r_mcangle_it 19.328 r_scbond_it 18.196 r_scbond_other 18.151 r_mcbond_it 14.596 r_mcbond_other 14.587 r_dihedral_angle_6_deg 14.12 r_dihedral_angle_3_deg 11.106 r_dihedral_angle_1_deg 7.179 r_dihedral_angle_2_deg 5.064 r_rigid_bond_restr 3.307 r_angle_refined_deg 1.314 r_angle_other_deg 0.444 r_nbd_refined 0.215 r_symmetry_nbd_other 0.198 r_symmetry_xyhbond_nbd_refined 0.198 r_nbtor_refined 0.185 r_nbd_other 0.181 r_ncsr_local_group_1 0.148 r_xyhbond_nbd_refined 0.128 r_xyhbond_nbd_other 0.116 r_symmetry_nbd_refined 0.095 r_symmetry_nbtor_other 0.08 r_chiral_restr 0.066 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3811 Nucleic Acid Atoms Solvent Atoms 204 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling PHASER phasing