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Structure and mechanism of the broad spectrum CRISPR-associated ring nuclease Crn4
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 4.5 293 0.1 M Sodium acetate pH 4.5
22 % v/v PEG Smear Broad
Crystal Properties Matthews coefficient Solvent content 2.35 47.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 116.314 α = 90 b = 116.314 β = 90 c = 38.863 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 XE 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 2.34 100.8 90.6 0.182 0.996 10.4 8 12327
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.34 2.38 0.375
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 2.34 100.731 12289 604 94.633 0.225 0.2221 0.227 0.2824 0.2851 40.675
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] 0.04 0.02 0.04 -0.131
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 12.355 r_dihedral_angle_3_deg 10.979 r_dihedral_angle_2_deg 8.211 r_dihedral_angle_1_deg 7.001 r_lrange_it 6.245 r_lrange_other 6.243 r_mcangle_it 3.61 r_mcangle_other 3.609 r_scangle_it 3.591 r_scangle_other 3.589
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 12.355 r_dihedral_angle_3_deg 10.979 r_dihedral_angle_2_deg 8.211 r_dihedral_angle_1_deg 7.001 r_lrange_it 6.245 r_lrange_other 6.243 r_mcangle_it 3.61 r_mcangle_other 3.609 r_scangle_it 3.591 r_scangle_other 3.589 r_mcbond_it 2.089 r_mcbond_other 2.086 r_scbond_it 2.063 r_scbond_other 2.061 r_angle_refined_deg 1.075 r_angle_other_deg 0.395 r_symmetry_nbd_refined 0.209 r_nbd_refined 0.208 r_symmetry_nbd_other 0.206 r_nbtor_refined 0.162 r_nbd_other 0.148 r_xyhbond_nbd_refined 0.146 r_ncsr_local_group_1 0.131 r_symmetry_xyhbond_nbd_refined 0.089 r_symmetry_nbtor_other 0.081 r_chiral_restr 0.047 r_gen_planes_refined 0.004 r_bond_refined_d 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1897 Nucleic Acid Atoms Solvent Atoms 93 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DIALS data reduction DIALS data scaling PHASER phasing