3LTR
5-OMe-dU containing DNA 8mer
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6 | 293 | 10% v / v MPD, 40 mM Na Cacodylate pH 6.0,12 mM Spermine tetra-HCl, 80 mM Sodium Chloride, 20 mM Magnesium Chloride, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.18 | 43.65 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 42.992 | α = 90 |
b = 42.992 | β = 90 |
c = 23.822 | 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 210 | Mirrors | 2009-07-15 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSLS BEAMLINE X12C | 0.9795 | NSLS | X12C |
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 | 1.3 | 50 | 91 | 0.06 | 36.7 | 21.5 | 5922 | 5389 |
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 | 1.3 | 1.35 | 58.1 | 0.381 | 2 | 5.5 | 275 |
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 (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 1DNS | 1.3 | 30.4 | 5612 | 5117 | 246 | 91.05 | 0.2026 | 0.20164 | 0.2224 | RANDOM | 13.098 |
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] | |
-0.25 | -0.25 | 0.5 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_scangle_it | 1.318 |
r_angle_refined_deg | 1.251 |
r_scbond_it | 0.895 |
r_nbtor_refined | 0.276 |
r_symmetry_vdw_refined | 0.187 |
r_nbd_refined | 0.158 |
r_xyhbond_nbd_refined | 0.151 |
r_symmetry_hbond_refined | 0.088 |
r_chiral_restr | 0.06 |
r_gen_planes_refined | 0.008 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | |
Nucleic Acid Atoms | 163 |
Solvent Atoms | 42 |
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 |