1YY0
Crystal structure of an RNA duplex containing a 2'-amine substitution and a 2'-amide product produced by in-crystal acylation at a C-A mismatch
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 8 | 273 | MPD, sodium cacodylate, spermidine, calcium chloride, magnesium chloride, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 273K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.07 | 40.68 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 42.6 | α = 90 |
b = 42.6 | β = 90 |
c = 121 | γ = 120 |
Symmetry | |
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Space Group | P 31 2 1 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | IMAGE PLATE | RIGAKU RAXIS IV | 2003-05-18 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym I (Observed) | 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 | 2.9 | 35.3 | 97.8 | 0.15 | 0.13 | 12.85 | 3530 | 3450 | 3 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
2.9 | 3 | 97.6 | 0.45 | 0.27 | 2.52 | 330 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 3.2 | 8.99 | 2225 | 2217 | 115 | 99.6 | 0.252 | 0.232 | 0.232 | 0.264 | RANDOM | 54 |
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] | |
11.32 | -1.18 | 11.32 | -22.64 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
c_dihedral_angle_d | 9.7 |
c_improper_angle_d | 1.46 |
c_angle_deg | 1.2 |
c_scangle_it | 1.08 |
c_scbond_it | 0.63 |
c_bond_d | 0.006 |
c_mcbond_it | |
c_mcangle_it |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | |
Nucleic Acid Atoms | 1011 |
Solvent Atoms | 8 |
Heterogen Atoms | 2 |
Software
Software | |
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Software Name | Purpose |
CNS | refinement |
CrystalClear | data reduction |
SCALEPACK | data scaling |
AMoRE | phasing |