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Crystal structure of the ADP-binding domain of the NAD+ riboswitch with N6-Methyl-adenosine-5'-triphosphate (m6ATP)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.2 280 0.2 M Potassium Chloride, 0.1 M Mg Acetate, 0.05 M Sodium Cacodylate pH 7.2, 10% w/v Polyethylene Glycol 3350
Crystal Properties Matthews coefficient Solvent content 5 75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.35 α = 90 b = 59.44 β = 90 c = 190.07 γ = 90
Symmetry Space Group I 2 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 PILATUS3 6M 2019-10-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.9186 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 2.3 47.52 99.17 0.051 0.023 0.999 16.1 6.3 27515 71.97
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 2.34 1.82 0.76 0.59 1
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 SAD FREE R-VALUE 2.3 47.52 1.34 27515 1391 98.69 0.2403 0.2394 0.2538 0.2571 0.2727 98.85
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 11.8046 f_angle_d 1.0987 f_chiral_restr 0.0488 f_plane_restr 0.0081 f_bond_d 0.0065
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 1111 Solvent Atoms 25 Heterogen Atoms 48
Software Software Software Name Purpose PHENIX refinement PHENIX refinement xia2 data reduction xia2 data scaling PHASER phasing