3IJN
5-SeMe-Cytidine modified DNA 8mer
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1DNS |
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 |
2.13 | 42.33 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 42.581 | α = 90 |
b = 42.581 | β = 90 |
c = 24.548 | 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 315r | 2009-07-15 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSLS BEAMLINE X29A | 0.9795 | NSLS | X29A |
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 | 30 | 97.8 | 0.07 | 38.16 | 15.6 | 2333 | 2282 |
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 | 1.86 | 85 | 0.445 | 2.89 | 4.6 | 187 |
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 | SAD | THROUGHOUT | 1DNS | 1.8 | 30 | 2211 | 2159 | 104 | 97.67 | 0.20729 | 0.20588 | 0.23421 | RANDOM | 12.118 |
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] | |
0.76 | 0.76 | -1.51 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_angle_refined_deg | 2.042 |
r_scangle_it | 0.814 |
r_scbond_it | 0.646 |
r_nbd_refined | 0.342 |
r_nbtor_refined | 0.279 |
r_symmetry_vdw_refined | 0.192 |
r_xyhbond_nbd_refined | 0.15 |
r_symmetry_hbond_refined | 0.135 |
r_chiral_restr | 0.067 |
r_bond_refined_d | 0.009 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | |
Nucleic Acid Atoms | 164 |
Solvent Atoms | 34 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
CBASS | data collection |
SHELXS | phasing |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |