280D
THE STRUCTURE OF AN RNA DODECAMER SHOWS HOW TANDEM U-U BASE PAIRS INCREASE THE RANGE OF STABLE RNA STRUCTURES AND THE DIVERSITY OF RECOGNITION SITES
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1SDR | HELIX 1 OF THE RNA DODECAMER CONTAINING THE E. COLI SHINE DALGARNO SEQUENCE (NDB ID ARL062) WITH THE SEQUENCE MUTATED TO R(GGCGCUUGCGUC). |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION | 7 | pH 7.00, VAPOR DIFFUSION |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.44 | 49.57 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 29.44 | α = 98.87 |
b = 28.91 | β = 72.95 |
c = 46.46 | γ = 96.16 |
Symmetry | |
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Space Group | P 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 | AREA DETECTOR | SIEMENS-NICOLET X100 | 1995-03-22 | M |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU RU200 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge 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 | 2.4 | 15 | 95.4 | 0.076 | 44.6 | 4.9 | 5429 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
2.4 | 2.6 | 95.5 | 0.182 | 8.05 | 2.4 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | HELIX 1 OF THE RNA DODECAMER CONTAINING THE E. COLI SHINE DALGARNO SEQUENCE (NDB ID ARL062) WITH THE SEQUENCE MUTATED TO R(GGCGCUUGCGUC). | 2.4 | 8 | 2 | 5142 | 0.191 | 0.191 | 0.24 |
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] | |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
x_dihedral_angle_d | 8 |
x_improper_angle_d | 1.5 |
x_angle_deg | 1.26 |
x_bond_d | 0.01 |
x_bond_d_na | |
x_bond_d_prot | |
x_angle_d | |
x_angle_d_na | |
x_angle_d_prot | |
x_angle_deg_na |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | |
Nucleic Acid Atoms | 1008 |
Solvent Atoms | 158 |
Heterogen Atoms |
Software
Software | |
---|---|
Software Name | Purpose |
AMoRE | phasing |
X-PLOR | refinement |
XDS | data reduction |
XSCALE | data scaling |