7OUO
Crystal structure of RNA duplex [UCGUGCGA]2 in complex with Ba2+ cation
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 293 | The crystal of the r(UCGUGCGA)2 duplex was obtained in the presence of its complementary strand UCGCACGA. The crystals grew in the 12th condition of nucleic acid mini-screen from Hampton (10% MPD, 0.040 M Sodium cacodylate trihydrate pH 6.0, 0.012 M Spermine tetrahydrochloride, 0.08M M Potassium chloride, 0.02M M Barium chloride) and further cryoprotected by 35% of MPD. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.24 | 45.11 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 44.003 | α = 90 |
b = 44.003 | β = 90 |
c = 122.312 | γ = 120 |
Symmetry | |
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Space Group | H 3 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 PILATUS 6M | 2018-07-09 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 22-BM | 1.000 | APS | 22-BM |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim 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 | 2.21 | 80 | 99.5 | 0.04 | 0.045 | 1 | 17.3 | 5.7 | 2460 |
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) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 2.21 | 2.35 | 1.12 | 1.24 | 0.81 | 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 (All) | R-Work | R-Free | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | model generated by Coot | 2.212 | 36.383 | 2459 | 123 | 99.434 | 0.236 | 0.2337 | 0.2857 | 70 |
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] | |
2.771 | 1.385 | 2.771 | -8.988 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_lrange_other | 8.452 |
r_lrange_it | 8.449 |
r_scangle_it | 6.738 |
r_scangle_other | 6.733 |
r_scbond_it | 5.229 |
r_scbond_other | 5.226 |
r_angle_refined_deg | 1.584 |
r_angle_other_deg | 1.401 |
r_symmetry_nbd_other | 0.273 |
r_nbtor_refined | 0.249 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | |
Nucleic Acid Atoms | 336 |
Solvent Atoms | 2 |
Heterogen Atoms | 1 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
XDS | data scaling |
PHASER | phasing |