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Structure of the alpha-N-methyltransferase (SonM) and RiPP precursor (SonA-I65W) heteromeric complex (bound to SAH)
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 2.17 43.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.13 α = 90.01 b = 108.02 β = 93.41 c = 58.59 γ = 89.95
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 2021-11-16 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 2.2 19.84 86.9 0.134 0.995 10.29 2.29 56305
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 0.476 0.935
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 19.84 53537 2767 86.82 0.29361 0.2918 0.3228 0.32685 0.3521 RANDOM 26.793
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] -7.77 10.72 0.63 7.8 -4.88 -0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.839 r_long_range_B_refined 6.162 r_long_range_B_other 6.158 r_dihedral_angle_1_deg 5.812 r_dihedral_angle_2_deg 5.811 r_scangle_other 3.998 r_mcangle_it 3.716 r_mcangle_other 3.716 r_scbond_it 2.558 r_scbond_other 2.558
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.839 r_long_range_B_refined 6.162 r_long_range_B_other 6.158 r_dihedral_angle_1_deg 5.812 r_dihedral_angle_2_deg 5.811 r_scangle_other 3.998 r_mcangle_it 3.716 r_mcangle_other 3.716 r_scbond_it 2.558 r_scbond_other 2.558 r_mcbond_it 2.464 r_mcbond_other 2.462 r_angle_refined_deg 0.849 r_angle_other_deg 0.271 r_chiral_restr 0.038 r_bond_refined_d 0.002 r_gen_planes_refined 0.002 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 9960 Nucleic Acid Atoms Solvent Atoms 170 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing