8TE0
16mer self-complementary duplex RNA with D:C pair sequence 1
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 | 293 | 10 mM Magnesium chloride hexahydrate, 50 mM HEPES sodium pH 7.0, 4.0 M Lithium chloride |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.22 | 44.49 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 42.501 | α = 90 |
b = 42.501 | β = 90 |
c = 129.967 | 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 | 99 | PIXEL | DECTRIS PILATUS3 6M | 2023-06-22 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ALS BEAMLINE 2.0.1 | 1.033216 | 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 | 1.42 | 50 | 96.2 | 0.065 | 0.069 | 0.024 | 0.983 | 30 | 7.1 | 8586 |
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 | 1.42 | 1.44 | 64.5 | 0.268 | 0.345 | 0.214 | 0.9 | 2.8 | 2 |
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 | 1.42 | 35.414 | 8160 | 379 | 91.398 | 0.216 | 0.2146 | 0.2376 | 11.558 |
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] | |
-0.001 | -0.001 | -0.001 | 0.004 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_lrange_it | 5.259 |
r_lrange_other | 5.02 |
r_angle_refined_deg | 2.37 |
r_scangle_it | 2.319 |
r_scangle_other | 2.317 |
r_scbond_it | 1.598 |
r_scbond_other | 1.596 |
r_angle_other_deg | 0.637 |
r_dihedral_angle_other_2_deg | 0.575 |
r_nbd_refined | 0.426 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | |
Nucleic Acid Atoms | 337 |
Solvent Atoms | 79 |
Heterogen Atoms | 1 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
PHASER | phasing |