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Crystal structure of B. subtilis Leucine tRNA with UAA anticodon
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model Other AlphaFold3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 297 0.072 M sodium chloride, 0.036 M sodium cacodylate trihydrate pH 7.0, 27% v/v (+/-)-2-methyl-2,4-pentanediol, 0.0108 M spermine tetrahydrochloride, 0.5% v/v ethyl acetate
Crystal Properties Matthews coefficient Solvent content 2.42 49.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.19 α = 90 b = 37.2 β = 99.45 c = 81.99 γ = 90
Symmetry Space Group P 1 21 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 EIGER2 X 9M 2024-05-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 7A (6B, 6C1) 0.9793 PAL/PLS 7A (6B, 6C1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim 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 2.499 33.796 91.6 0.112 0.123 0.05 0.997 9.7 6.1 8962
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.499 2.542 99.6 1.945 2.123 0.839 0.62 1 6.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.5 33.796 8502 459 91.54 0.21861 0.21626 0.2205 0.26328 0.2704 RANDOM 57.492
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] -4.72 -1.17 -3.19 7.87
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 9.307 r_long_range_B_other 9.305 r_scangle_other 7.851 r_scbond_it 5.409 r_scbond_other 5.408 r_angle_refined_deg 1.899 r_angle_other_deg 0.535 r_chiral_restr 0.066 r_gen_planes_refined 0.013 r_bond_refined_d 0.006
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 9.307 r_long_range_B_other 9.305 r_scangle_other 7.851 r_scbond_it 5.409 r_scbond_other 5.408 r_angle_refined_deg 1.899 r_angle_other_deg 0.535 r_chiral_restr 0.066 r_gen_planes_refined 0.013 r_bond_refined_d 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_dihedral_angle_1_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 1866 Solvent Atoms Heterogen Atoms 14
Software Software Software Name Purpose MxDC data collection autoPROC data processing autoPROC data reduction XSCALE data scaling MOLREP phasing Coot model building REFMAC refinement PDB_EXTRACT data extraction