3IXN
Crystal structure of d(CCGGTACCGG) as B-DNA duplex
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7 | 293 | 5mM CoCl2, 1mM spermine, 50% MPD, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.44 | 49.56 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 32.94 | α = 90 |
b = 32.94 | β = 90 |
c = 94.854 | γ = 120 |
Symmetry | |
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Space Group | P 61 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | CCD | MAR CCD 165 mm | Double Crystal | 2009-06-26 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ELETTRA BEAMLINE 5.2R | 1.54 | ELETTRA | 5.2R |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym 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 | 2.87 | 30 | 99.4 | 0.094 | 0.081 | 6.2 | 10.1 | 1378 | 1365 | 69.9 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
2.87 | 2.97 | 97.8 | 0.286 | 0.279 | 1.2 | 10.8 | 135 |
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 | Fiber model built in INSIGHTII software | 2.87 | 28.53 | 1365 | 1160 | 63 | 91.2 | 0.26212 | 0.26146 | 0.27469 | RANDOM | 39.728 |
Temperature Factor Modeling | ||||||
---|---|---|---|---|---|---|
Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
-16.39 | -16.39 | 32.77 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_scangle_it | 7.405 |
r_scbond_it | 5.568 |
r_angle_refined_deg | 3.964 |
r_chiral_restr | 0.227 |
r_bond_refined_d | 0.025 |
r_gen_planes_refined | 0.018 |
r_bond_other_d | |
r_angle_other_deg | |
r_dihedral_angle_1_deg | |
r_dihedral_angle_2_deg |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | |
Nucleic Acid Atoms | 404 |
Solvent Atoms | 11 |
Heterogen Atoms | 3 |
Software
Software | |
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Software Name | Purpose |
MAR345dtb | data collection |
AMoRE | phasing |
REFMAC | refinement |
AUTOMAR | data reduction |
SCALEPACK | data scaling |