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The X-ray structure of N-terminal catalytic domain of Thermoplasma acidophilum tRNA methyltransferase Trm56 (Ta0931) in complex with 5'-Methylthioadenosine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2YY8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 293 PEG3350, Bis-Tris
Crystal Properties Matthews coefficient Solvent content 2.92 57.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.7 α = 90 b = 71.4 β = 90 c = 86.99 γ = 90
Symmetry Space Group C 2 2 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 16M 2023-02-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.0 SPring-8 BL41XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.99 50 99.4 0.069 1 22.19 5.9 10241
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.99 2.11 98 0.28 0.97 8.57
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2YY8 1.992 39.083 10241 512 99.485 0.173 0.1709 0.1832 0.2243 0.2348 24.892
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] -1.054 2.16 -1.106
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.012 r_dihedral_angle_6_deg 16.49 r_dihedral_angle_3_deg 15.402 r_dihedral_angle_1_deg 7.17 r_lrange_it 7.145 r_lrange_other 7.142 r_scangle_it 5.325 r_scangle_other 5.322 r_scbond_it 3.761 r_scbond_other 3.758
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.012 r_dihedral_angle_6_deg 16.49 r_dihedral_angle_3_deg 15.402 r_dihedral_angle_1_deg 7.17 r_lrange_it 7.145 r_lrange_other 7.142 r_scangle_it 5.325 r_scangle_other 5.322 r_scbond_it 3.761 r_scbond_other 3.758 r_mcangle_it 3.319 r_mcangle_other 3.317 r_mcbond_it 2.347 r_mcbond_other 2.338 r_angle_refined_deg 1.595 r_angle_other_deg 0.56 r_nbd_refined 0.236 r_symmetry_nbd_refined 0.236 r_symmetry_xyhbond_nbd_refined 0.225 r_xyhbond_nbd_refined 0.218 r_symmetry_nbd_other 0.197 r_nbtor_refined 0.187 r_nbd_other 0.186 r_symmetry_nbtor_other 0.08 r_symmetry_xyhbond_nbd_other 0.08 r_chiral_restr 0.075 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1222 Nucleic Acid Atoms Solvent Atoms 53 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing