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PreQ1-1 (type-1) riboswitch with stacked metabolites and a C10-G34 base pair in the expression platform
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7REX Chain A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 30% PEG 8000, 0.2 M ammonium acetate, 0.01 M magnesium acetate tetrahydrate, and 0.05 M sodium cacodylate pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.1 41.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.867 α = 90 b = 67.612 β = 100.53 c = 50.589 γ = 90
Symmetry Space Group P 1 21 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 2022-03-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 0.97 SSRL BL12-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 35.2 99 0.051 7.6 5.3 5588 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3 3.2 92.2 0.339 1.4 5.3
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3 35.16 1.36 5478 548 97.32 0.2286 0.2245 0.2243 0.2651 0.2657 random 111.8
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 15.685 f_angle_d 0.726 f_chiral_restr 0.028 f_plane_restr 0.003 f_bond_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 2071 Solvent Atoms 6 Heterogen Atoms 3
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHENIX phasing