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Structure of the alpha-N-methyltransferase (SonM) and RiPP precursor (SonA-L63D) heteromeric complex
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 8% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.62 53.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.27 α = 90 b = 92.27 β = 90 c = 162.35 γ = 120
Symmetry Space Group P 32 2 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 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-B 1.033167 APS 23-ID-B
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 2.35 19.83 98.4 0.069 1 36.32 12.05 33473
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 2.35 2.45 1.339 0.703
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 2.35 19.83 31799 1674 98.39 0.19263 0.19007 0.2009 0.24013 0.242 RANDOM 81.939
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] 0.12 0.06 0.12 -0.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.094 r_long_range_B_other 13.035 r_long_range_B_refined 13.026 r_scangle_other 11.461 r_scbond_it 8.383 r_scbond_other 8.381 r_dihedral_angle_2_deg 8.096 r_mcangle_other 7.37 r_mcangle_it 7.368 r_mcbond_it 5.989
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.094 r_long_range_B_other 13.035 r_long_range_B_refined 13.026 r_scangle_other 11.461 r_scbond_it 8.383 r_scbond_other 8.381 r_dihedral_angle_2_deg 8.096 r_mcangle_other 7.37 r_mcangle_it 7.368 r_mcbond_it 5.989 r_mcbond_other 5.978 r_dihedral_angle_1_deg 4.902 r_angle_refined_deg 0.565 r_angle_other_deg 0.188 r_chiral_restr 0.025 r_bond_refined_d 0.001 r_gen_planes_refined 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 4811 Nucleic Acid Atoms Solvent Atoms 127 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing