3IKI
5-SMe-dU containing DNA octamer
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7 | 293 | 10% v / v MPD, 40 mM Na Cacodylate pH 7.0, 12 mM Spermine tetra-HCl, 40 mM Lithium Chloride, 80 mM Strontium Chloride / 20 mM Magnesium Chloride, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.15 | 42.67 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 42.882 | α = 90 |
b = 42.882 | β = 90 |
c = 23.687 | 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 | 99 | CCD | ADSC QUANTUM 4 | 2008-10-22 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSLS BEAMLINE X12B | 0.9795 | NSLS | X12B |
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 | 1.38 | 50 | 94 | 0.057 | 23.02 | 8.4 | 4911 | 4616 |
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 | 1.38 | 1.43 | 67.8 | 0.245 | 5.86 | 5.2 | 324 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 1DNS | 1.38 | 30.32 | 4650 | 4373 | 216 | 94.04 | 0.17907 | 0.17838 | 0.19414 | RANDOM | 12.133 |
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] | |
0.12 | 0.12 | -0.24 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_angle_refined_deg | 1.467 |
r_scangle_it | 1.249 |
r_scbond_it | 0.825 |
r_nbd_refined | 0.371 |
r_nbtor_refined | 0.277 |
r_symmetry_vdw_refined | 0.18 |
r_xyhbond_nbd_refined | 0.102 |
r_symmetry_hbond_refined | 0.083 |
r_chiral_restr | 0.057 |
r_bond_refined_d | 0.007 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | |
Nucleic Acid Atoms | 163 |
Solvent Atoms | 38 |
Heterogen Atoms | 1 |
Software
Software | |
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Software Name | Purpose |
CBASS | data collection |
PHASES | phasing |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |