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Crystal Structure of a prebiotic tRNA acceptor stem mimic
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 292 FUSION (Molecular Dimensions Ltd) was used for screening crystallization conditions by the sitting drop vapor diffusion method (Gorrec & Bellini, 2022). Solutions containing the RNA samples (1 mM) in 100 mM HEPES buffer pH 8 and 10 mM MgCl2 were heated at 65 degrees C for 2 minutes, then cooled slowly to room temperature. The RNA solutions were mixed with FUSION solution in a 1:1 ratio for crystallization.
Crystal Properties Matthews coefficient Solvent content 2.26 45.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 32.007 α = 90 b = 32.007 β = 90 c = 281.333 γ = 120
Symmetry Space Group P 65 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 80 PIXEL DECTRIS EIGER2 XE 16M 2023-12-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.916 Diamond I04
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 2.5 46.89 100 0.088 0.09 0.02 1 24.8 33.2 3624
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) 2.5 2.6 100 6.622 6.783 1.462 0.388 0.6 35.8
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 (All) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD FREE R-VALUE 2.52 46.889 3396 158 98.179 0.259 0.2577 0.2955 0.2959 RANDOM 83.243
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] -0.227 -0.113 -0.227 0.735
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 13.083 r_lrange_other 13.081 r_scangle_it 6.846 r_scangle_other 6.842 r_scbond_it 4.442 r_scbond_other 4.442 r_angle_refined_deg 1.265 r_angle_other_deg 0.383 r_dihedral_angle_other_2_deg 0.301 r_nbtor_refined 0.248
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 13.083 r_lrange_other 13.081 r_scangle_it 6.846 r_scangle_other 6.842 r_scbond_it 4.442 r_scbond_other 4.442 r_angle_refined_deg 1.265 r_angle_other_deg 0.383 r_dihedral_angle_other_2_deg 0.301 r_nbtor_refined 0.248 r_nbd_other 0.236 r_symmetry_xyhbond_nbd_refined 0.223 r_symmetry_nbd_other 0.216 r_xyhbond_nbd_refined 0.169 r_nbd_refined 0.108 r_symmetry_nbd_refined 0.082 r_symmetry_nbtor_other 0.078 r_chiral_restr 0.056 r_symmetry_xyhbond_nbd_other 0.036 r_gen_planes_refined 0.008 r_bond_refined_d 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 604 Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose XDS data scaling PHENIX phasing REFMAC refinement Coot model building