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Structure of the alpha-N-methyltransferase (SonM) and RiPP precursor (SonA-Y62A) heteromeric complex (bound to SAH - structure 1)
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 and 22% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.27 45.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.17 α = 90 b = 111.48 β = 96.83 c = 85.54 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 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 2.2 60.28 99.8 0.073 0.999 14.43 5.45 68051
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 2.2 2.3 0.761 0.815
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 2.2 60.28 64647 3403 99.78 0.18215 0.18023 0.1894 0.21898 0.2257 RANDOM 51.051
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] 0.52 -0.9 0.62 -0.9
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.507 r_long_range_B_other 9.68 r_long_range_B_refined 9.677 r_scangle_other 8.009 r_dihedral_angle_1_deg 5.65 r_scbond_it 5.343 r_scbond_other 5.342 r_dihedral_angle_2_deg 5.113 r_mcangle_it 5.1 r_mcangle_other 5.099
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.507 r_long_range_B_other 9.68 r_long_range_B_refined 9.677 r_scangle_other 8.009 r_dihedral_angle_1_deg 5.65 r_scbond_it 5.343 r_scbond_other 5.342 r_dihedral_angle_2_deg 5.113 r_mcangle_it 5.1 r_mcangle_other 5.099 r_mcbond_it 3.702 r_mcbond_other 3.7 r_angle_refined_deg 0.752 r_angle_other_deg 0.252 r_chiral_restr 0.037 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 9853 Nucleic Acid Atoms Solvent Atoms 253 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing