5DER
RNA oligonucleotide containing (R)-C5'-ME-2'F U
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 5.5 | 293 | 40 mM sodium cacodylate, 20 mM hexamine Co(III) chloride, 12 mM NaCl, 80 mM KCl, reservoir 40% MPD |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.08 | 40.85 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 44.116 | α = 90 |
b = 44.116 | β = 90 |
c = 86.927 | γ = 90 |
Symmetry | |
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Space Group | P 43 21 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 | CCD | Bruker Platinum 135 | Montel multilayer, confocal mirrors | 2014-09-30 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | BRUKER AXS MICROSTAR | 1.54178 |
Data Collection
Overall | |||||||||||||||||||
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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 | 1.8 | 25.34 | 99.6 | 0.099 | 9.57 | 4.9 | 15381 |
Highest Resolution Shell | |||||||||||||||||||
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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) | |||||||||||
1 | 1.8 | 1.89 | 97.7 | 0.406 | 1.77 | 2.73 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | 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 | FREE R-VALUE | 1.8 | 25.34 | 0.143 | 15118 | 454 | 99.6375140051 | 0.248 | 0.257 | 0.274 | 22.4012714523 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 15.1239428142 |
f_angle_d | 0.85631665895 |
f_chiral_restr | 0.0335223668827 |
f_bond_d | 0.00419357466461 |
f_plane_restr | 0.00184552964032 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | |
Nucleic Acid Atoms | 672 |
Solvent Atoms | 194 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
PROTEUM PLUS | data collection |
PHENIX | refinement |
PDB_EXTRACT | data extraction |
PROTEUM PLUS | data reduction |
PROTEUM PLUS | data scaling |
PHENIX | phasing |