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Structure and catalytic mechanism of SAM-AMP lyase in Clostridium botulinum CorA-associated type III CRISPR system
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 7.5 293 70% MPD
0.1M HEPES pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.27 45.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.396 α = 75.74 b = 55.396 β = 72.011 c = 81.658 γ = 60.82
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 PILATUS 6M-F 2023-09-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.9212 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.7 48.1 97.6 0.999 3.6 3.6 84447
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 1.7 1.73 0.565
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 MOLECULAR REPLACEMENT THROUGHOUT 1.7 48.089 84414 4259 97.562 0.21 0.2087 0.2168 0.2365 0.2471 RANDOM 40.006
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] 0.366 -0.32 -0.887 -0.264 0.345 -0.626
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.151 r_dihedral_angle_3_deg 13.022 r_lrange_it 8.264 r_lrange_other 8.264 r_scangle_it 6.883 r_scangle_other 6.883 r_dihedral_angle_1_deg 6.12 r_scbond_it 4.708 r_scbond_other 4.708 r_mcangle_other 4.464
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.151 r_dihedral_angle_3_deg 13.022 r_lrange_it 8.264 r_lrange_other 8.264 r_scangle_it 6.883 r_scangle_other 6.883 r_dihedral_angle_1_deg 6.12 r_scbond_it 4.708 r_scbond_other 4.708 r_mcangle_other 4.464 r_mcangle_it 4.462 r_dihedral_angle_2_deg 4.051 r_mcbond_it 3.482 r_mcbond_other 3.482 r_angle_refined_deg 1.552 r_angle_other_deg 0.524 r_nbd_other 0.295 r_symmetry_nbd_refined 0.217 r_nbd_refined 0.203 r_symmetry_nbd_other 0.199 r_symmetry_xyhbond_nbd_other 0.193 r_nbtor_refined 0.168 r_symmetry_xyhbond_nbd_refined 0.127 r_xyhbond_nbd_refined 0.11 r_ncsr_local_group_5 0.085 r_ncsr_local_group_15 0.083 r_symmetry_nbtor_other 0.079 r_chiral_restr 0.077 r_ncsr_local_group_8 0.076 r_ncsr_local_group_2 0.075 r_ncsr_local_group_9 0.074 r_ncsr_local_group_6 0.073 r_ncsr_local_group_14 0.072 r_ncsr_local_group_10 0.07 r_ncsr_local_group_12 0.067 r_ncsr_local_group_7 0.066 r_ncsr_local_group_13 0.066 r_ncsr_local_group_4 0.06 r_ncsr_local_group_11 0.06 r_ncsr_local_group_1 0.058 r_ncsr_local_group_3 0.053 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5936 Nucleic Acid Atoms Solvent Atoms 224 Heterogen Atoms 56
Software Software Software Name Purpose REFMAC refinement DIALS data reduction DIALS data scaling PHASER phasing