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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 1.35 A resolution (P212121 - form I)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2R3S
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.2 M ammonium formate, 20% (w/v) PEG 3350, Additive: 0.002 M S-Adenosyl methionine (SAM/AdoMet)
Crystal Properties Matthews coefficient Solvent content 1.96 37.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.059 α = 90 b = 78.229 β = 90 c = 131.68 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 1.311 67.256 94.2 0.0506 0.0527 0.0146 0.999 19.4 12.43 101542
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) 1.311 1.429 62.5 0.7081 0.7878 0.3382 0.806 1.71 5.2 5080
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 2r3s 1.35 33.63 1.35 100565 4933 69.1 0.167 0.166 0.1671 0.19 0.1911 26.47
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 12.17 f_angle_d 0.801 f_chiral_restr 0.066 f_plane_restr 0.008 f_bond_d 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5458 Nucleic Acid Atoms Solvent Atoms 551 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