6CK5
PRPP riboswitch from T. mathranii bound to PRPP
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 5T83 | PDB entry 5T83 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | MICROBATCH | 5.6 | 303.15 | 150 uM RNA in 10 mM magnesium chloride, 10 mM potassium chloride, 10 mM HEPES-KOH, pH 7.5, 10 mM PRPP, mixed 2:1 with 80 mM sodium chloride, 20 mM barium chloride dihydrate, 40 mM sodium cacodylate trihydrate, pH 5.6, 45% v/v MPD, 12 mM spermine tetrahydrachloride. Crystals were flash-frozen without further preparation. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.73 | 54.99 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 33.977 | α = 90 |
b = 89.575 | β = 96.9 |
c = 136.367 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 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 | 2017-10-13 | 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 | 2.5 | 40 | 98.2 | 0.1 | 0.118 | 0.061 | 9.3 | 3.6 | 27959 |
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 | 2.5 | 2.54 | 98.9 | 1.068 | 1.246 | 0.633 | 0.176 | 3.9 |
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 | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB entry 5T83 | 2.49 | 37.35 | 26309 | 1361 | 96.98 | 0.2164 | 0.2145 | 0.2523 | RANDOM | 78.592 |
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] | |
51.63 | -31.18 | 8.9 | -60.53 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_angle_refined_deg | 1.842 |
r_angle_other_deg | 1.769 |
r_chiral_restr | 0.115 |
r_gen_planes_refined | 0.014 |
r_bond_refined_d | 0.009 |
r_bond_other_d | 0.004 |
r_gen_planes_other | 0.002 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | |
Nucleic Acid Atoms | 4418 |
Solvent Atoms | 52 |
Heterogen Atoms | 75 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
HKL-2000 | data scaling |
PDB_EXTRACT | data extraction |
PHASER | phasing |
SCALEPACK | data scaling |
Coot | model building |
HKL-2000 | data reduction |