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Crystal structure of a methyltransferase involved in the biosynthesis of gentamicin in complex with the methylated Kanamycin B
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5U4T
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291 Calcium chloride, Hepes pH 8, Peg 6000
Crystal Properties Matthews coefficient Solvent content 2.05 40.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.045 α = 90 b = 70.052 β = 90 c = 86.008 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 298 PIXEL DECTRIS PILATUS 2M 2016-10-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON LNLS BEAMLINE W01B-MX2 1.45 LNLS W01B-MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.932 43.896 97.26 0.023 21.76 2 23107
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 5U4T 1.932 43.896 1.35 23101 1168 97.27 0.1787 0.1763 0.1794 0.2243 0.2278 18.1266
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 11.638 f_angle_d 0.994 f_chiral_restr 0.054 f_bond_d 0.007 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2381 Nucleic Acid Atoms Solvent Atoms 175 Heterogen Atoms 61
Software Software Software Name Purpose PHENIX refinement PDB_EXTRACT data extraction XDS data reduction Aimless data scaling PHASER phasing