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Crystal structure of RNA device 43 truncation mutant 3 (U100C), holo state
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other hybrid model constructed using accession codes 3egz and 3zp8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 0.05 M HEPES pH 7.5, 0.01 M MgCl2, 2.5 mM Spermine, 14% MPD
Crystal Properties Matthews coefficient Solvent content 3.69 66.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.223 α = 90 b = 81.223 β = 90 c = 528.831 γ = 90
Symmetry Space Group P 43 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 PIXEL DECTRIS PILATUS3 6M 2022-10-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97918 APS 19-ID
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 3.06 528.84 100 0.09 0.095 0.029 0.997 10.8 12.2 35158
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 3.06 3.21 100 2.148 2.239 0.625 0.464 12.8
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 3.06 44.32 1.33 35012 1770 99.97 0.2266 0.2249 0.2249 0.2573 0.2578 168.2
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 15.175 f_angle_d 0.48 f_chiral_restr 0.025 f_plane_restr 0.002 f_bond_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 9392 Solvent Atoms 21 Heterogen Atoms 61
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing