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RhoBAST RNA aptamer in complex with the SpyRho555 analogue, MaP555
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9BUN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 292 40 mM MES, 10 mM barium chloride, 80 mM potassium chloride, 25% MPD, 12 mM spermine tetrahydrochloride
Crystal Properties Matthews coefficient Solvent content 2.88 57.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.529 α = 90 b = 54.818 β = 103.263 c = 83.513 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 PILATUS 200K 2024-09-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE RIGAKU MICROMAX-003 1.54178
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) Rpim I (All) 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 2.8 20 98 0.127 0.074 9.4 2.7 8812
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.8 2.9 96.2 0.127 0.074 0.815 2.69 2.4
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.8 19.27 21.83 8303 848 98.03 0.2629 0.2539 0.2513 0.2706 0.2699 Random 73.1
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 19.8034 f_angle_d 0.4954 f_chiral_restr 0.0336 f_plane_restr 0.0042 f_bond_d 0.0015
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 2072 Solvent Atoms 34 Heterogen Atoms 47
Software Software Software Name Purpose PHENIX refinement HKL-3000 data reduction HKL-3000 data scaling PHASER phasing