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Crystal structure of tRNA (guanine-N(1)-)-methyltransferase with bound SAH from Mycobacterium smegmatis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5ZHI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 287 MysmA.00937.a.AE1.PW38670 at 19.05 mg/ml, incubated with 5 mM SAH, mixed 1:1 with MCSG1(a10): 28% (v/v) PPG P400, 0.1 M HEPES:NaOH, pH = 7.5, 0.2 M CaCl2. Tray: 311562a10. Puck: dcp5-10.
Crystal Properties Matthews coefficient Solvent content 1.92 35.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.1 α = 90 b = 59.1 β = 90 c = 114.55 γ = 90
Symmetry Space Group P 43 21 2
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 RIGAKU SATURN 944+ 2019-10-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.5418
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 50 98.4 0.037 0.038 1 55.1 24.126 14157 44.465
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 2.05 99.9 0.621 0.642 0.987 4.76 16.159
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 5ZHI 2 41.79 1.34 14147 1373 98.37 0.2087 0.203 0.208 0.2629 0.2704 49.38
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 18.0736 f_angle_d 0.8053 f_chiral_restr 0.0523 f_bond_d 0.0062 f_plane_restr 0.0045
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1557 Nucleic Acid Atoms Solvent Atoms 60 Heterogen Atoms 26
Software Software Software Name Purpose XDS data reduction XSCALE data scaling PHASER phasing PHENIX refinement PDB_EXTRACT data extraction