8FER
16mer self-complementary duplex RNA with two continuous s(2)U:s(2)U pairs
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3ND4 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 293 | 0.02 M Magnesium chloride hexahydrate, 0.002 M Cobalt(II) chloride hexahydrate, 0.05 M HEPES sodium pH 7.5, 2.0 M Ammonium sulfate, 0.001 M Spermine |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.34 | 47.46 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 43.81 | α = 90 |
b = 43.81 | β = 90 |
c = 258.17 | 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 PILATUS3 6M | 2022-09-14 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ALS BEAMLINE 2.0.1 | 1.037690 | ALS | 2.0.1 |
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) | 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 | 1.54 | 50 | 99.7 | 0.113 | 0.121 | 0.043 | 0.986 | 13.7 | 7.9 | 14744 |
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 | 1.54 | 1.57 | 100 | 0.429 | 0.461 | 0.166 | 0.978 | 4.4 | 7.6 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | 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 | THROUGHOUT | 1.54 | 43.065 | 14221 | 725 | 96.101 | 0.221 | 0.2187 | 0.2587 | 14.69 |
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] | |
0.002 | 0.001 | 0.002 | -0.007 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_angle_other_deg | 3.873 |
r_lrange_it | 3.249 |
r_lrange_other | 3.248 |
r_angle_refined_deg | 2.757 |
r_scangle_it | 2.216 |
r_scangle_other | 2.215 |
r_chiral_restr_other | 2.028 |
r_scbond_it | 1.593 |
r_scbond_other | 1.592 |
r_symmetry_nbd_other | 0.249 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | |
Nucleic Acid Atoms | 668 |
Solvent Atoms | 85 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
PHASER | phasing |