8FEO
16mer self-complementary duplex RNA with two separated native U: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 | 293 | 0.08 M Strontium chloride hexahydrate, 0.02 M Magnesium chloride hexahydrate, 0.04 M Sodium cacodylate trihydrate pH 7.0, 20% v/v (+/-)-2-Methyl-2,4-pentanediol, 0.012 M Spermine tetrahydrochloride |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.05 | 40.06 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 41.503 | α = 90 |
b = 41.503 | β = 90 |
c = 125.299 | 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 EIGER X 16M | 2022-04-23 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 23-ID-B | 1.033175 | APS | 23-ID-B |
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 | 1.52 | 17.8 | 98.3 | 0.075 | 0.081 | 0.029 | 0.998 | 36.4 | 8.4 | 6587 |
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 | 1.52 | 1.55 | 99.1 | 0.234 | 0.253 | 0.093 | 0.973 | 3 | 7 |
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 | 1.52 | 17.796 | 6587 | 320 | 98.182 | 0.2 | 0.198 | 0.2393 | 21.388 |
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] | |
0.008 | 0.004 | 0.008 | -0.027 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_lrange_other | 4.636 |
r_lrange_it | 4.62 |
r_angle_refined_deg | 2.559 |
r_scangle_it | 2.358 |
r_scangle_other | 2.356 |
r_scbond_it | 1.722 |
r_scbond_other | 1.719 |
r_angle_other_deg | 0.688 |
r_nbd_other | 0.414 |
r_nbtor_refined | 0.238 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | |
Nucleic Acid Atoms | 334 |
Solvent Atoms | 73 |
Heterogen Atoms | 2 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
xia2 | data reduction |
DIALS | data scaling |
PHASER | phasing |