6S7D
Self-complementary duplex DNA containing an internucleoside phosphoroselenolate
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6 | 291 | The crystallization solution contained 1 uL of 2 mM oligonucleotide and 6 uL of a solution containing 10% (v/v) 2-methyl-2,4-pentanediol, 40 mM Na-cacodylate pH 6, 12 mM Spermine tetra-HCl, 80 mM NaCl and 20 mM BaCl2. This was equilibrated against 100 uL of 35% (v/v) 2-methyl-2,4-pentanediol. Crystals grew in approximately 1-2 weeks and were grown using the sitting-drop method at 291 K. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.14 | 60.8 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 38.642 | α = 90 |
b = 38.642 | β = 90 |
c = 79.307 | 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 | PIXEL | DECTRIS PILATUS3 6M | 2019-02-18 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I03 | 0.9596 | Diamond | I03 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | 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 | 1.45 | 25.57 | 98.4 | 0.05 | 0.06 | 0.032 | 0.998 | 12.5 | 3 | 12548 | -3 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 1.45 | 1.47 | 98.7 | 0.556 | 0.674 | 0.375 | 0.741 | 2.9 |
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 | SAD | FREE R-VALUE | 1.45 | 25.57 | 3.79 | 12530 | 579 | 98.31 | 0.1919 | 0.1849 | 0.2366 | 25.54 |
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 | 20.1052 |
f_angle_d | 0.9357 |
f_chiral_restr | 0.0785 |
f_plane_restr | 0.0092 |
f_bond_d | 0.0089 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | |
Nucleic Acid Atoms | 404 |
Solvent Atoms | 60 |
Heterogen Atoms | 19 |
Software
Software | |
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Software Name | Purpose |
Coot | model building |
PHENIX | refinement |
xia2 | data scaling |
DIALS | data reduction |
SHELXCD | phasing |