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SAM-I riboswitch bearing the H. marismortui Kt-7 variant 3bn is UA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5FK3 PDB ENTRY 5FK3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 40 MM NA-CACODYLATE (PH 7.0), 80 MM KCL, 30 MM BACL2, 12 MM SPERMINE-HCL, 12% (V/V) MPD
Crystal Properties Matthews coefficient Solvent content 1.99 38.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.77 α = 90 b = 61.77 β = 90 c = 153.928 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 173 PIXEL DECTRIS PIXEL 2014-02-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 61.77 100 0.19 8.2 14.5 6437 1.2 81.01
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.8 2.95 100 1.5 1.2 14.2
Refinement Statistics Diffraction ID Structure Solution Method Starting model 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 PDB ENTRY 5FK3 3 57.326 1.34 6437 601 99.6 0.2358 0.2327 0.246 0.2934 0.301 121.35
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 17.523 f_angle_d 0.61 f_chiral_restr 0.034 f_plane_restr 0.005 f_bond_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 2030 Solvent Atoms Heterogen Atoms 41
Software Software Software Name Purpose PHENIX refinement iMOSFLM data reduction Aimless data scaling PHASER phasing