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The structure of the G. violaceus guanidine II riboswitch P1 stem-loop with guanidine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5NEO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 280 0.15 M KCl 25% v/v Glycerol 0.05M Bis-Tris 7.0
1.6M Ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 3.36 63.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.7 α = 90 b = 55.7 β = 90 c = 132.58 γ = 120
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 2017-03-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.9201 Diamond I24
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.93 44.193 99.3 0.084 0.029 0.999 16.4 9.4 11476 1.3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.93 1.96 100 1.75 0.594 0.564 1.3 9.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation 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 THROUGHOUT 5NEO 1.93 44.193 1.34 11476 564 99.19 0.1988 0.1974 0.2294 0.2236 0.2539
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 10.186 f_angle_d 2.336 f_chiral_restr 0.091 f_bond_d 0.018 f_plane_restr 0.018
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 386 Solvent Atoms 27 Heterogen Atoms 11
Software Software Software Name Purpose PHENIX refinement xia2 data reduction xia2 data scaling PHENIX phasing