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The X-ray structure of N-terminal catalytic domain of Thermoplasma acidophilum tRNA methyltransferase Trm56 (Ta0931).
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 = 110.074 α = 90 b = 110.074 β = 90 c = 57.728 γ = 120
Symmetry Space Group P 32 2 1
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 4M 2022-07-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL26B1 1.0 SPring-8 BL26B1
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 1.8 50 98.7 0.051 0.053 0.9990000000000001 30.43 5.3 36948
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 1.8 1.91 0.387 0.401 0.97
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2yy8 1.802 36.03 36939 1847 98.701 0.167 0.1654 0.2024 0.2166 RANDOM 30.909
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] 0.005 0.002 0.005 -0.015
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 18.219 r_dihedral_angle_6_deg 16.747 r_dihedral_angle_3_deg 15.024 r_lrange_other 7.544 r_lrange_it 7.539 r_dihedral_angle_1_deg 6.664 r_scangle_it 6.22 r_scangle_other 6.219 r_scbond_it 4.45 r_scbond_other 4.448
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 18.219 r_dihedral_angle_6_deg 16.747 r_dihedral_angle_3_deg 15.024 r_lrange_other 7.544 r_lrange_it 7.539 r_dihedral_angle_1_deg 6.664 r_scangle_it 6.22 r_scangle_other 6.219 r_scbond_it 4.45 r_scbond_other 4.448 r_mcangle_other 3.777 r_mcangle_it 3.776 r_mcbond_it 2.966 r_mcbond_other 2.966 r_angle_refined_deg 1.7 r_angle_other_deg 0.619 r_symmetry_nbd_refined 0.296 r_nbd_refined 0.238 r_symmetry_xyhbond_nbd_refined 0.235 r_xyhbond_nbd_refined 0.217 r_symmetry_nbd_other 0.185 r_nbtor_refined 0.184 r_nbd_other 0.16 r_chiral_restr 0.091 r_symmetry_nbtor_other 0.081 r_bond_refined_d 0.011 r_gen_planes_refined 0.01 r_bond_other_d 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2416 Nucleic Acid Atoms Solvent Atoms 125 Heterogen Atoms 8
Software Software Software Name Purpose REFMAC refinement XDS data scaling XDS data reduction PHASER phasing