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Structure of the alpha-N-methyltransferase (SonM) and RiPP precursor (SonA with QSY deletion) 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 292 240 mM sodium malonate pH 5-5.5, 8-12% PEG 3350 at a 1-1 or 2-1 ratio of protein to mother liquor. Protein concentration is 20mg/mL.
Crystal Properties Matthews coefficient Solvent content 2.22 44.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.39 α = 90 b = 108.73 β = 93.66 c = 59.14 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 X 6M 2022-03-03 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 52.28 99.7 0.111 0.997 10.89 5.41 44465
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 2.1 0.582 1
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 52.28 42244 2224 99.67 0.2045 0.20273 0.2117 0.23814 0.2444 RANDOM 24.852
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] 0.06 -0.08 -0.28 0.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 9.746 r_long_range_B_refined 7.407 r_long_range_B_other 7.213 r_dihedral_angle_1_deg 5.214 r_scangle_other 4.656 r_scbond_it 3.024 r_scbond_other 3.024 r_mcangle_it 2.686 r_mcangle_other 2.686 r_mcbond_it 1.857
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 9.746 r_long_range_B_refined 7.407 r_long_range_B_other 7.213 r_dihedral_angle_1_deg 5.214 r_scangle_other 4.656 r_scbond_it 3.024 r_scbond_other 3.024 r_mcangle_it 2.686 r_mcangle_other 2.686 r_mcbond_it 1.857 r_mcbond_other 1.855 r_dihedral_angle_2_deg 1.641 r_angle_refined_deg 0.553 r_angle_other_deg 0.292 r_chiral_restr 0.028 r_bond_other_d 0.011 r_bond_refined_d 0.002 r_gen_planes_refined 0.002 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 5032 Nucleic Acid Atoms Solvent Atoms 544 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing