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Crystal Structure of the O-Methyltransferase TomG from Streptomyces achromogenes involved in Tomaymycin synthesis in complex with SAM
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3CBG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.3 295 2.1 M NH4(SO4)2, 0.1 M Li2SO4, 0.1 M Hepes pH 7.3
Crystal Properties Matthews coefficient Solvent content 2.26 45.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.597 α = 90 b = 75.877 β = 90 c = 86.784 γ = 90
Symmetry Space Group P 21 21 21
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 PILATUS 6M 2016-11-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, DESY BEAMLINE P11 1.033 PETRA III, DESY P11
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 1.55 50.47 99.6 0.079 1 22.9 13.2 65091
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 1.55 1.58 98.7 1.691 0.783 1.7 13 3142
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3cbg 1.55 50.47 1.35 65001 1622 99.4 0.1486 0.1482 0.1532 0.1661 0.1704
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 15.433 f_angle_d 0.715 f_chiral_restr 0.046 f_bond_d 0.004 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3434 Nucleic Acid Atoms Solvent Atoms 488 Heterogen Atoms 121
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling Aimless data scaling PHASER phasing Coot model building PHENIX refinement