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Crystal structure of E. coli Leucine tRNA with UAG 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 4.6 297 0.25 M ammonium sulfate, 0.1 M sodium acetate trihydrate, pH 4.6, 32% (w/v) polyethylene glycol monomethyl ether 2000
Crystal Properties Matthews coefficient Solvent content 3.44 64.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.365 α = 90 b = 114.179 β = 90 c = 53.817 γ = 90
Symmetry Space Group P 21 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 ADSC QUANTUM 270 2023-04-13 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 2.897 48.681 86.8 0.191 0.2 0.059 0.997 11.1 11.5 4225
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 2.897 3.331 61.7 1.75 1.821 0.498 0.626 1.8 13.2
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 2.9 48.681 4000 218 48.04 0.24762 0.24644 0.2463 0.26961 0.2692 RANDOM 84.52
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] -3.27 -0.09 3.36
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 20.927 r_scbond_it 7.399 r_angle_refined_deg 1.68 r_chiral_restr 0.078 r_gen_planes_refined 0.008 r_bond_refined_d 0.005 r_bond_other_d r_angle_other_deg r_dihedral_angle_1_deg r_dihedral_angle_2_deg
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 20.927 r_scbond_it 7.399 r_angle_refined_deg 1.68 r_chiral_restr 0.078 r_gen_planes_refined 0.008 r_bond_refined_d 0.005 r_bond_other_d r_angle_other_deg r_dihedral_angle_1_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_gen_planes_other 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_scbond_other r_scangle_it r_scangle_other r_long_range_B_other 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 1737 Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose JBluIce-EPICS data collection autoPROC data processing autoPROC data reduction STARANISO data scaling MOLREP phasing REFMAC refinement Coot model building PDB_EXTRACT data extraction