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Crystal structure of NAD-II riboswitch (single strand) with NMN
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8HB1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 291 0.012 M Sodium chloride,
0.08 M Potassium chloride
0.04 M Sodium cacodylate trihydrate pH 5.5
45% v/v (+/-)-2-Methyl-2,4-pentanediol
0.02 M Hexammine cobalt(III) chloride
Soaking with BaCl2
Crystal Properties Matthews coefficient Solvent content 5.6 78.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 121.362 α = 90 b = 121.362 β = 90 c = 109.055 γ = 90
Symmetry Space Group I 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 EIGER X 16M 2021-11-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.9785 SSRF BL19U1
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 2.3 50 93.2 0.082 0.017 1 26.6 13.3 17176 1 70.63
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 2.3 2.42 3.4 0.75 0.642 1
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 8HB1 2.3 27.26 1.33 17080 853 92.87 0.2284 0.2271 0.2282 0.2531 0.2542 93.23
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 16.4374 f_angle_d 0.6382 f_chiral_restr 0.0302 f_plane_restr 0.0039 f_bond_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 1167 Solvent Atoms Heterogen Atoms 51
Software Software Software Name Purpose PHENIX refinement autoPROC data reduction SCALA data scaling PHASER phasing