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Structure of the alpha-N-methyltransferase (SonM mutant Y93F) and RiPP precursor (SonA) heteromeric complex (no cofactor)
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 were concentrated at 20 mg/mL and crystallized at pH ranging between 5.5-7 and using PEG 3,350 (0-20%) as precipitant
Crystal Properties Matthews coefficient Solvent content 2.27 45.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.34 α = 90 b = 108.71 β = 93.92 c = 58.96 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 1.033167 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 2.1 58.82 99.2 0.998 17.5 5.41 38054
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 2.1 2.2 0.997
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 2.1 58.82 36150 1903 99.15 0.1855 0.1832 0.1961 0.2292 0.2395 RANDOM 20.587
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] -1.14 0.19 2.43 -1.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.827 r_dihedral_angle_3_deg 13.921 r_dihedral_angle_4_deg 12.842 r_dihedral_angle_1_deg 6.724 r_angle_refined_deg 1.646 r_angle_other_deg 1.446 r_chiral_restr 0.075 r_bond_refined_d 0.012 r_gen_planes_refined 0.01 r_gen_planes_other 0.004
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.827 r_dihedral_angle_3_deg 13.921 r_dihedral_angle_4_deg 12.842 r_dihedral_angle_1_deg 6.724 r_angle_refined_deg 1.646 r_angle_other_deg 1.446 r_chiral_restr 0.075 r_bond_refined_d 0.012 r_gen_planes_refined 0.01 r_gen_planes_other 0.004 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5138 Nucleic Acid Atoms Solvent Atoms 1007 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XSCALE data scaling MOLREP phasing