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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 5.5 293 23.8% PEG3350, 0.2M magnesium chloride, 0.1M bis-Tris pH 5.5
Crystal Properties Matthews coefficient Solvent content 2.5 50.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.271 α = 90 b = 102.899 β = 103.881 c = 72.442 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 S 16M 2024-07-05 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 1.44 102.9 100 0.068 0.998 11.2 6.9 169690
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 1.44 1.47 2.101 0.299
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 1.441 70.425 166107 1951 97.868 0.222 0.222 0.2296 0.2395 0.2457 28.045
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] -0.655 0.469 -0.734 1.031
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 13.849 r_dihedral_angle_3_deg 9.58 r_dihedral_angle_1_deg 5.877 r_dihedral_angle_2_deg 4.915 r_lrange_it 4.299 r_lrange_other 4.275 r_mcangle_it 2.086 r_mcangle_other 2.086 r_scangle_it 2.069 r_scangle_other 2.069
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 13.849 r_dihedral_angle_3_deg 9.58 r_dihedral_angle_1_deg 5.877 r_dihedral_angle_2_deg 4.915 r_lrange_it 4.299 r_lrange_other 4.275 r_mcangle_it 2.086 r_mcangle_other 2.086 r_scangle_it 2.069 r_scangle_other 2.069 r_scbond_it 1.207 r_scbond_other 1.207 r_mcbond_it 1.193 r_mcbond_other 1.193 r_angle_refined_deg 0.987 r_angle_other_deg 0.425 r_dihedral_angle_other_2_deg 0.336 r_nbd_other 0.219 r_nbd_refined 0.206 r_symmetry_nbd_other 0.195 r_nbtor_refined 0.167 r_symmetry_xyhbond_nbd_refined 0.122 r_xyhbond_nbd_refined 0.101 r_symmetry_nbd_refined 0.093 r_symmetry_nbtor_other 0.081 r_ncsr_local_group_6 0.076 r_ncsr_local_group_4 0.075 r_ncsr_local_group_12 0.075 r_ncsr_local_group_14 0.074 r_ncsr_local_group_3 0.073 r_ncsr_local_group_9 0.073 r_ncsr_local_group_15 0.071 r_ncsr_local_group_5 0.07 r_ncsr_local_group_7 0.069 r_ncsr_local_group_10 0.067 r_ncsr_local_group_1 0.066 r_ncsr_local_group_11 0.066 r_ncsr_local_group_13 0.062 r_ncsr_local_group_2 0.059 r_ncsr_local_group_8 0.051 r_chiral_restr 0.046 r_bond_refined_d 0.003 r_gen_planes_refined 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 5626 Nucleic Acid Atoms 396 Solvent Atoms 693 Heterogen Atoms 7
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling PHASER phasing