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G96A mutant of the PRPP riboswitch from T. mathranii bound to ppGpp
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 7.5 296.15 1 uL 150 uM RNA in 10 mM magnesium chloride, 10 mM potassium chloride, 10 mM HEPES-KOH, pH 7.5, 1 mM ppGpp, mixed with 0.8 uL 80 mM sodium chloride, 40 mM sodium cacodylate, pH 7.0, 30% MPD, 12 mM spermine
Crystal Properties Matthews coefficient Solvent content 2.7 54.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.252 α = 91.18 b = 62.147 β = 89.61 c = 125.909 γ = 101.94
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 2017-12-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.97918 APS 24-ID-E
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 3.097 40 93.7 0.099 0.13 0.082 3.9 2.2 26741 97.77
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.1 3.15 94.7 1.222 1.604 1.026 0.253 2.1
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 MOLECULAR REPLACEMENT THROUGHOUT 3.097 36.539 1.96 26642 1263 92.77 0.2509 0.2484 0.2482 0.3041 0.3022 144.6331
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 19.556 f_angle_d 1.852 f_chiral_restr 0.137 f_bond_d 0.018 f_plane_restr 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 8829 Solvent Atoms 21 Heterogen Atoms 191
Software Software Software Name Purpose SCALEPACK data scaling PHASER phasing PHENIX refinement REFMAC refinement PDB_EXTRACT data extraction Coot model building HKL-2000 data scaling HKL-2000 data reduction