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Crystal structure of 2'-dG riboswitch
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8KEB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291 0.04 M Lithium chloride,
0.08 M Strontium chloride hexahydrate,
0.02 M Magnesium chloride hexahydrate
0.04 M Sodium cacodylate trihydrate pH 7.0
30% v/v (+/-)-2-Methyl-2,4-pentanediol
0.012 M Spermine tetrahydrochloride
Crystal Properties Matthews coefficient Solvent content 2.15 42.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.73 α = 113.83 b = 51.275 β = 114.99 c = 52.484 γ = 90.05
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 2022-03-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.97853 SSRF BL19U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 3.01 33.61 97.3 0.957 2.9 3.4 7298 70.75
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.01 3.09 0.779
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 3.01 27.34 1.99 7023 362 93.58 0.3177 0.3172 0.3258 0.3271 0.3374 110.05
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 15.3432 f_angle_d 0.7336 f_chiral_restr 0.0328 f_plane_restr 0.0051 f_bond_d 0.0027
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 2922 Solvent Atoms Heterogen Atoms 38
Software Software Software Name Purpose PHENIX refinement PHENIX refinement xia2 data scaling PHASER phasing xia2 data reduction