7TZT
Crystal structure of the E. coli thiM riboswitch in complex with N1,N1-dimethyl-N2-(quinoxalin-6-ylmethyl)ethane-1,2-diamine (linked compound 37)
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 291 | The RNA (0.15 mM) was incubated in a buffer containing 5 mM Tris-HCl, pH 8.0, 3 mM MgCl2, 10 mM NaCl, 0.1 M KCl, and 0.5 mM spermine with 1.0 mM compound 38. Reservoir solution was 50 mM Bis-Tris, pH 6.5, 0.5 M ammonium chloride, 15 mm MnCl2, and 28% (v/v) PEG2000 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.06 | 40.36 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 61.018 | α = 90 |
b = 61.018 | β = 90 |
c = 102.855 | γ = 120 |
Symmetry | |
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Space Group | P 32 1 2 |
Diffraction
Diffraction Experiment | ||||||||||||||
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ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | PIXEL | DECTRIS EIGER2 X 16M | 2021-03-21 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 24-ID-C | 0.9791 | APS | 24-ID-C |
Data Collection
Overall | |||||||||||||||||||
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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 | 2.93 | 50 | 99.9 | 0.13 | 0.044 | 0.995 | 304.8 | 10 | 4715 | 97.5 |
Highest Resolution Shell | |||||||||||||||||||
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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 | 2.93 | 2.98 | 100 | 3.612 | 1.14 | 0.637 | 5.5 | 10.6 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 2HOJ | 2.96 | 47 | 1.36 | 4715 | 4715 | 98.19 | 0.2445 | 0.2434 | 0.257 | 115.66 |
Temperature Factor Modeling | ||||||
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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 | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 16.6256 |
f_angle_d | 0.6046 |
f_chiral_restr | 0.0326 |
f_plane_restr | 0.0048 |
f_bond_d | 0.002 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | |
Nucleic Acid Atoms | 1655 |
Solvent Atoms | |
Heterogen Atoms | 14 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
HKL-2000 | data scaling |
HKL-2000 | data reduction |
PHASER | phasing |
Coot | model building |