6CK4
G96A mutant of the PRPP riboswitch from T. mathranii bound to ppGpp
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | MICROBATCH | 7.5 | 296.15 | 1 uL 150 uM RNA in 10 mM magnesium chloride, 10 mM potassium chloride, 10 mM HEPES-KOH, pH 7.5, 1 mM ppGpp, mixed with 0.8 uL 80 mM sodium chloride, 40 mM sodium cacodylate, pH 7.0, 30% MPD, 12 mM spermine |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.7 | 54.47 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 53.252 | α = 91.18 |
b = 62.147 | β = 89.61 |
c = 125.909 | γ = 101.94 |
Symmetry | |
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Space Group | P 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 EIGER X 16M | 2017-12-10 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 24-ID-E | 0.97918 | APS | 24-ID-E |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | 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 | 3.097 | 40 | 93.7 | 0.099 | 0.13 | 0.082 | 3.9 | 2.2 | 26741 | 97.77 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 3.1 | 3.15 | 94.7 | 1.222 | 1.604 | 1.026 | 0.253 | 2.1 |
Refinement
Statistics | |||||||||||||||||||
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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 | R-Free | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 3.097 | 36.539 | 1.96 | 26642 | 1263 | 92.77 | 0.2509 | 0.2484 | 0.3041 | 144.6331 |
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 | 19.556 |
f_angle_d | 1.852 |
f_chiral_restr | 0.137 |
f_bond_d | 0.018 |
f_plane_restr | 0.01 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | |
Nucleic Acid Atoms | 8829 |
Solvent Atoms | 21 |
Heterogen Atoms | 191 |
Software
Software | |
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Software Name | Purpose |
SCALEPACK | data scaling |
PHASER | phasing |
PHENIX | refinement |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
Coot | model building |
HKL-2000 | data scaling |
HKL-2000 | data reduction |