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Structure of the alpha-N-methyltransferase (SonM) and RiPP precursor (SonA-I65W) 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 with 14% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.2 44.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.2 α = 96 b = 59.1 β = 112.4 c = 59.3 γ = 93.4
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 EIGER X 16M 2021-11-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 1.033167 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 2.1 29.22 88.5 0.08 0.995 10.64 2.29 33547
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.2 0.327 0.911
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 2.1 29.22 31868 1678 88.68 0.2116 0.20962 0.219 0.24889 0.2568 RANDOM 33.644
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] -2.03 -0.92 0.08 -0.25 0.49 1.55
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.286 r_long_range_B_refined 5.983 r_long_range_B_other 5.954 r_dihedral_angle_1_deg 5.599 r_scangle_other 4.077 r_mcangle_other 2.933 r_mcangle_it 2.932 r_dihedral_angle_2_deg 2.806 r_scbond_it 2.596 r_scbond_other 2.595
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.286 r_long_range_B_refined 5.983 r_long_range_B_other 5.954 r_dihedral_angle_1_deg 5.599 r_scangle_other 4.077 r_mcangle_other 2.933 r_mcangle_it 2.932 r_dihedral_angle_2_deg 2.806 r_scbond_it 2.596 r_scbond_other 2.595 r_mcbond_it 2.008 r_mcbond_other 1.999 r_angle_refined_deg 0.655 r_angle_other_deg 0.216 r_chiral_restr 0.032 r_gen_planes_refined 0.002 r_bond_refined_d 0.001 r_bond_other_d r_dihedral_angle_4_deg r_gen_planes_other 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 4954 Nucleic Acid Atoms Solvent Atoms 343 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing