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Crystal structure of NAD-II riboswitch (single strand) with NAD
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 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
Crystal Properties Matthews coefficient Solvent content 2.16 43.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.756 α = 90 b = 68.64 β = 90 c = 114.009 γ = 90
Symmetry Space Group P 21 21 21
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 2021-09-20 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 2.64 19.61 99.2 0.052 0.016 0.919 23.3 11.99 9135 2
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 2.64 2.74 94.3 0.897 0.292 0.919 2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 8HB1 2.64 19.61 8168 934 98.89 0.2339 0.2294 0.2348 0.27456 0.2518 RANDOM 103.385
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] 10.64 -4.23 -6.41
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 9.374 r_long_range_B_other 9.374 r_scangle_other 4.045 r_scbond_it 2.5 r_scbond_other 2.5 r_angle_refined_deg 1.749 r_angle_other_deg 1.677 r_chiral_restr 0.104 r_gen_planes_refined 0.012 r_bond_refined_d 0.01
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 9.374 r_long_range_B_other 9.374 r_scangle_other 4.045 r_scbond_it 2.5 r_scbond_other 2.5 r_angle_refined_deg 1.749 r_angle_other_deg 1.677 r_chiral_restr 0.104 r_gen_planes_refined 0.012 r_bond_refined_d 0.01 r_bond_other_d 0.003 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 2111 Solvent Atoms Heterogen Atoms 154
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing