6UC7
Structure of guanine riboswitch bound to N2-acetyl guanine
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 4FE5 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 297 | 10 mM potassium HEPES pH 7.5, 20% v/v PEG 3000 MW, 30 mM cobalt hexamine, 600 mM ammonium acetate. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.24 | 45.12 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 132.107 | ¦Á = 90 |
b = 35.082 | ¦Â = 90.99 |
c = 41.606 | ¦Ã = 90 |
Symmetry | |
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Space Group | C 1 2 1 |
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 PILATUS 200K | 2018-12-03 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU MICROMAX-007 HF | 1.5406 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym I (Observed) | Rrim 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 | 1.798 | 19.74 | 93.83 | 0.066 | 0.079 | 0.079 | 19.3 | 3 | 16940 | 19.24 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||
1 | 1.798 | 1.862 | 56.89 | 0.182 | 0.182 | 0.232 | 0.142 | 0.903 | 3.05 | 1.9 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | 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 | 4FE5 | 1.798 | 19.74 | 16922 | 3062 | 88.97 | 0.1837 | 0.2093 |
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] | |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | |
Nucleic Acid Atoms | 1422 |
Solvent Atoms | 224 |
Heterogen Atoms | 70 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
HKL-3000 | data reduction |
HKL-3000 | data scaling |
PHASER | phasing |