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Protein 2A from Theiler's murine encephalomyelitis virus (TMEV) bound to RNA pseudoknot
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7NBV placed first; partial solution in silico model AlphaFold predicted 7 base-pair stem 2; placed second
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.9 294 150 nL 2A-RNA complex (7.5 mg/mL, 693 uM) in 10 mM HEPES pH 7.4, 100 mM NaCl, 1 mM MgCl2, 1 mM DTT was mixed with 150 nL 0.2 M ammonium acetate, 0.1 M Bis-Tris pH 5.9, 19% (w/v) PEG 3350.
Crystal Properties Matthews coefficient Solvent content 3.26 62.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 104.191 α = 90 b = 45.931 β = 127.34 c = 65.72 γ = 90
Symmetry Space Group C 1 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 EIGER2 XE 16M 2024-10-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9537 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 1.9 52.25 98.7 0.152 0.166 0.065 0.974 7.1 6.5 19441 20.15
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 1.9 1.94 98.3 0.728 0.792 0.308 0.64 3.3 6.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.9 52.25 1.33 19410 894 98.59 0.1948 0.1931 0.1955 0.2295 0.2301 33.2
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 13.3552 f_angle_d 0.8313 f_chiral_restr 0.0547 f_plane_restr 0.0124 f_bond_d 0.0094
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1030 Nucleic Acid Atoms 635 Solvent Atoms 249 Heterogen Atoms
Software Software Software Name Purpose GDA data collection xia2 data reduction XDS data reduction Aimless data scaling PHASER phasing PHENIX refinement Coot model building