8HCH
Crystal structure of mTREX1-Uridine complex
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 293 | 12.5% v/v MPD; 12.5% PEG 1000; 12.5% w/v PEG 3350, 0.2% w/v Cytidine, 0.2% w/v Inosine, 0.2% w/v Ribavirin, 0.2% w/v Thymidine, 0.2% w/v Uridine, 0.1M Imidazole, 0.1M MES monohydrate (acid), pH6.5 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.2 | 44.22 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 67.632 | α = 90 |
b = 81.149 | β = 103.51 |
c = 93.653 | 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 | CCD | ADSC QUANTUM 315r | 2020-03-17 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSRRC BEAMLINE BL13B1 | 1.00000 | NSRRC | BL13B1 |
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 | 30 | 99.6 | 0.063 | 0.071 | 0.034 | 12.4 | 4.3 | 66457 | 32.63 |
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 | 2.03 | 99.6 | 0.495 | 0.572 | 0.28 | 0.725 | 3.9 |
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 | THROUGHOUT | 5YWS | 2 | 24.69 | 1.37 | 66275 | 5114 | 99.55 | 0.1901 | 0.187 | 0.2275 | 46.4932 |
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 | 6757 |
Nucleic Acid Atoms | |
Solvent Atoms | 438 |
Heterogen Atoms | 140 |
Software
Software | |
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Software Name | Purpose |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
MOLREP | phasing |
PHENIX | refinement |
PDB_EXTRACT | data extraction |