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Class I type III preQ1 riboswitch from E. coli
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 293 31% MPD, 0.05 M Na-cacodylate pH 6.0, 0.012 spermine-HCl, 0.1 M KCl and 0.002 M MgCl2, 0.005 M MnCl2-tetrahydrate
Crystal Properties Matthews coefficient Solvent content 2.01 38.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.739 α = 90 b = 32.272 β = 96.93 c = 51.206 γ = 90
Symmetry Space Group P 1 2 1
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 6M Flat Si Rh coated M0, Kirkpatrick-Baez flat bent Si M1 & M2 2022-03-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 1.8500 SSRL BL12-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 36.53 98.1 0.024 0.999 16.7 22 12805 -3 52.92
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.38 97.9 0.271 0.917 2.8 16.3
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 36.53 1.34 12805 1282 97.1 0.2099 0.2053 0.2068 0.2522 0.2559 58.31
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 13.5876 f_angle_d 0.4647 f_chiral_restr 0.0227 f_plane_restr 0.0026 f_bond_d 0.0016
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 1167 Solvent Atoms 31 Heterogen Atoms 30
Software Software Software Name Purpose Blu-Ice data collection XDS data reduction Aimless data scaling PHENIX phasing Coot model building PHENIX model building PHENIX refinement