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Structure of the heteromeric complex between the alpha-N-methyltransferase (SonM) and a truncated construct of the RiPP precursor (SonA) (with SAM)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5N0P
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 proteins at 20 mg/mL and crystallized in 100 mM Bis-Tris at pH 5.5 with 100 mM ammonium acetate and 4-7% PEG 10000
Crystal Properties Matthews coefficient Solvent content 2.35 47.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.24 α = 90 b = 112.86 β = 97.82 c = 85.87 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 EIGER X 16M 2020-03-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 0.991840 APS 23-ID-B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.75 56.43 98.3 0.983 24.88 4.29 134823
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.75 1.85 0.974
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 5N0P 1.75 56.43 128081 6742 98.33 0.1889 0.1873 0.1965 0.219 0.2284 RANDOM 30.189
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] 0.07 0.01 -0.01 -0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.561 r_dihedral_angle_4_deg 16.766 r_dihedral_angle_3_deg 14.876 r_dihedral_angle_1_deg 6.052 r_angle_other_deg 2.259 r_angle_refined_deg 1.123 r_chiral_restr 0.045 r_bond_other_d 0.035 r_gen_planes_other 0.004 r_gen_planes_refined 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.561 r_dihedral_angle_4_deg 16.766 r_dihedral_angle_3_deg 14.876 r_dihedral_angle_1_deg 6.052 r_angle_other_deg 2.259 r_angle_refined_deg 1.123 r_chiral_restr 0.045 r_bond_other_d 0.035 r_gen_planes_other 0.004 r_gen_planes_refined 0.003 r_bond_refined_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9753 Nucleic Acid Atoms Solvent Atoms 993 Heterogen Atoms 78
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XSCALE data scaling MOLREP phasing