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Crystal structure of MfnG, an L- and D-tyrosine O-methyltransferase from the marformycin biosynthesis pathway of Streptomyces drozdowiczii, with SAH bound at 1.2 A resolution (P212121 - form II)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7UX6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 293 0.1 M Tris pH 8, 30% Polyethylene glycol monomethyl ether (PEG MME) 2000, Additive: 0.002 M S-Adenosyl methionine (SAM/AdoMet)
Crystal Properties Matthews coefficient Solvent content 2.1 41.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.694 α = 90 b = 86.334 β = 90 c = 134.504 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 EIGER X 9M 2021-02-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 0.9762 APS 21-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim 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 1.139 72.655 89.6 0.143 0.1452 0.0248 0.996 15.13 32.75 214260 11.85
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.139 1.204 42.5 1.5681 1.6026 0.3222 0.727 2.17 23.24 10668
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 THROUGHOUT 7UX6 1.14 35.18 1.35 214231 10679 83.4 0.121 0.119 0.1192 0.142 0.1416 18.98
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 13.968 f_angle_d 1.35 f_chiral_restr 0.099 f_plane_restr 0.015 f_bond_d 0.013
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5690 Nucleic Acid Atoms Solvent Atoms 861 Heterogen Atoms 70
Software Software Software Name Purpose PHENIX refinement autoPROC data processing XDS data reduction Aimless data scaling STARANISO data scaling PHASER phasing PDB_EXTRACT data extraction