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Crystal structure of a tRNA (guanine-N1)-methyltransferase from Acinetobacter baumannii AB5075-UW bound to S-adenosyl homocysteine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1UAL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 287 AcbaC.00054.a.B1.PW38905 at 26 mg/mL with 6 mM GMP and 6 mM SAH against Morpheus condition F2 with 10% PEG 8000, 20% ethylene glycol, 0.1 M MES/imidazole pH 6.5, 0.02 M each glucose, mannose, galactose, fucose, xylose, acetyl-glucosamine, direct cryo, unique puck ID okj1-10, crystal tracking ID 319640f2
Crystal Properties Matthews coefficient Solvent content 2.53 51.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.96 α = 90 b = 65.96 β = 90 c = 132.59 γ = 90
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD RAYONIX MX-300 2021-02-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.9787 APS 21-ID-F
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.4 46.64 100 0.04 0.043 1 25.84 6.328 22187 56.43
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.46 100 0.524 0.571 0.91 3.69 6.387
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 1ual 2.4 46.64 1.36 22132 2057 99.92 0.185 0.181 0.1809 0.2252 0.2248 71.293
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]
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3601 Nucleic Acid Atoms Solvent Atoms 59 Heterogen Atoms 52
Software Software Software Name Purpose XDS data reduction XSCALE data scaling MOLREP phasing PHENIX refinement PDB_EXTRACT data extraction