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Crystal structure of a class I PreQ1 riboswitch complexed with a synthetic compound
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6E1S
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 293 0.1M potassium sodium tartrate, 0.1M sodium citrate (pH 5.6), 2.6M ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 5.53 77.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 116.39 α = 90 b = 116.39 β = 90 c = 57.78 γ = 120
Symmetry Space Group P 63 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 PILATUS 6M 2020-04-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL45XU 1.0 SPring-8 BL45XU
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 2.25 41 99.9 0.064 0.012 0.999 32.4 31.2 11424
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 2.25 2.39 99.9 3.62 0.641 0.589 1.44 31.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (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 2.25 41 11405 570 99.92 0.198 0.2094 0.214 0.2215 Random selection 96.87
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 15.2885 f_angle_d 0.3731 f_chiral_restr 0.0191 f_plane_restr 0.0034 f_bond_d 0.0016
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 663 Solvent Atoms 5 Heterogen Atoms 20
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing