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Structure of the alpha-N-methyltransferase (SonM) and RiPP precursor (SonA-Y62A) heteromeric complex (bound to SAM)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7LTE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 298 240 mM sodium malonate pH 5.5, 12% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.37 48.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.25 α = 95.77 b = 58.96 β = 112.61 c = 59.23 γ = 93.88
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 PILATUS3 6M 2023-02-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 1.0332 APS 23-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) 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 1.5 45.99 92.3 0.092 0.994 9.49 2.74 95561
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 1.5 1.6 0.54 0.799
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 1.5 45.99 90783 4778 92.5 0.16538 0.16349 0.1728 0.20121 0.2101 RANDOM 19.174
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] -1.58 -0.44 -0.18 1.83 0.42 -0.15
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 14.329 r_long_range_B_other 13.8 r_dihedral_angle_3_deg 13.287 r_scangle_other 9.87 r_mcangle_it 7.267 r_mcangle_other 7.266 r_scbond_it 6.821 r_scbond_other 6.819 r_dihedral_angle_1_deg 5.791 r_mcbond_it 5.109
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 14.329 r_long_range_B_other 13.8 r_dihedral_angle_3_deg 13.287 r_scangle_other 9.87 r_mcangle_it 7.267 r_mcangle_other 7.266 r_scbond_it 6.821 r_scbond_other 6.819 r_dihedral_angle_1_deg 5.791 r_mcbond_it 5.109 r_mcbond_other 5.093 r_rigid_bond_restr 3.953 r_dihedral_angle_2_deg 3.801 r_angle_refined_deg 0.921 r_angle_other_deg 0.341 r_chiral_restr 0.049 r_gen_planes_refined 0.003 r_bond_refined_d 0.002 r_gen_planes_other 0.001 r_bond_other_d 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_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4931 Nucleic Acid Atoms Solvent Atoms 346 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing