1YZD
Crystal structure of an RNA duplex containing a site specific 2'-amine substitution at a C-G Watson-Crick base pair
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, magnesium chloride, calcium chloride, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 273K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.11 | 41.76 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 43 | α = 90 |
b = 43 | β = 90 |
c = 121 | γ = 120 |
Symmetry | |
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Space Group | P 31 2 1 |
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 | IMAGE PLATE | RIGAKU RAXIS IV++ | 2004-02-24 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU |
Data Collection
Overall | |||||||||||||||||||
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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 | 2.18 | 31.7 | 91.4 | 0.077 | 0.06 | 15.2 | 21.79 | 7277 | 6646 | 1 | 28.7 |
Highest Resolution Shell | |||||||||||||||||||
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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) | ||||||||||
2.18 | 2.28 | 57.4 | 0.387 | 0.37 | 3.37 | 405 |
Refinement
Statistics | |||||||||||||||||||
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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 | 2.35 | 8.07 | 5567 | 5556 | 301 | 98 | 0.265 | 0.236 | 0.236 | 0.292 | RANDOM | 30.5 |
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] | |
4.45 | 2.19 | 4.45 | -8.91 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
c_dihedral_angle_d | 6.9 |
c_scangle_it | 1.92 |
c_scbond_it | 1.46 |
c_improper_angle_d | 1.33 |
c_angle_deg | 0.9 |
c_bond_d | 0.005 |
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 | 29 |
Heterogen Atoms | 1 |
Software
Software | |
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Software Name | Purpose |
CNS | refinement |
CrystalClear | data reduction |
SCALEPACK | data scaling |
AMoRE | phasing |