☰ Navigation Tabs
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 293 70% MPD, 0.1M HEPES pH7.5
Crystal Properties Matthews coefficient Solvent content 2.27 45.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.794 α = 87.7 b = 55.484 β = 72.62 c = 81.972 γ = 61.01
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 2023-09-22 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) 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 1.65 46.044 97.5 0.094 0.998 10.6 7.2 92147
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 1.65 1.68 95.9 0.627 6.5
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 (Observed) 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 1.65 46.04 87290 4746 97.43 0.19058 0.18882 0.2014 0.22393 0.2362 RANDOM 26.288
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] -2.1 0.62 -0.9 -0.95 0.69 2.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.834 r_long_range_B_refined 6.542 r_long_range_B_other 6.44 r_dihedral_angle_1_deg 6.137 r_dihedral_angle_2_deg 5.952 r_scangle_other 5.33 r_scbond_it 3.436 r_scbond_other 3.436 r_mcangle_other 3.226 r_mcangle_it 3.225
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.834 r_long_range_B_refined 6.542 r_long_range_B_other 6.44 r_dihedral_angle_1_deg 6.137 r_dihedral_angle_2_deg 5.952 r_scangle_other 5.33 r_scbond_it 3.436 r_scbond_other 3.436 r_mcangle_other 3.226 r_mcangle_it 3.225 r_mcbond_it 2.263 r_mcbond_other 2.259 r_angle_refined_deg 1.524 r_angle_other_deg 0.527 r_chiral_restr 0.074 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6254 Nucleic Acid Atoms Solvent Atoms 511 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DIALS data reduction DIALS data scaling PHASER phasing