1Z79
Crystal structure of an RNA duplex containing site specific 2'-amine substitution at a C-A mismatch (at pH 5)
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 5.2 | 273 | MPD, Na cacodylate, spermine, calcium chloride, pH 5.2, VAPOR DIFFUSION, SITTING DROP, temperature 273K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.14 | 42.41 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 43 | α = 90 |
b = 43 | β = 90 |
c = 122 | 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++ | 2003-02-14 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
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 | 2.5 | 23 | 98.6 | 0.08 | 0.1 | 11.65 | 14.29 | 4979 | 4904 | 1 | 60.4 |
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) | ||||||||||
2.5 | 2.59 | 100 | 0.5 | 0.419 | 2.86 | 465 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | 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 | 1YRM | 2.55 | 8.08 | 4436 | 248 | 99.3 | 0.217 | 0.217 | 0.217 | 0.262 | RANDOM | 38.6 |
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] | |
7.13 | 2.72 | 7.13 | -14.26 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
c_dihedral_angle_d | 6.9 |
c_scangle_it | 1.85 |
c_improper_angle_d | 1.37 |
c_scbond_it | 1.36 |
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 | 1008 |
Solvent Atoms | 34 |
Heterogen Atoms | 1 |
Software
Software | |
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Software Name | Purpose |
CNS | refinement |
CrystalClear | data reduction |
SCALEPACK | data scaling |
CNS | phasing |