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Structural basis for 2'-deoxyguanosine recognition by the 2'-dG-II class of riboswitches
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4FE5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 303 40 mM sodium cacodylate pH 6.0, 23% v/v methylpentanediol, 18 mM cobalt hexamine, 80 mM potassium chloride, and 12 mM sodium chloride
Crystal Properties Matthews coefficient Solvent content 3.67 66.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.805 α = 90 b = 91.805 β = 90 c = 77.756 γ = 90
Symmetry Space Group P 41 2 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 PILATUS 200K 2018-06-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5406
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.803 29.953 97.69 0.096 0.03 27.25 10.8 8547 58.19
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 2.803 2.904 97.69 0.608 0.195 0.946 3.37 10.3
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 FREE R-VALUE 4FE5 2.803 29.953 1.33 8547 843 98.17 0.2474 0.2443 0.2478 0.2756 0.2768
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 14.997 f_angle_d 0.535 f_chiral_restr 0.024 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 1478 Solvent Atoms 12 Heterogen Atoms 59
Software Software Software Name Purpose PHENIX refinement HKL-3000 data reduction HKL-3000 data scaling PHASER phasing