4R6M
Crystal Structure of DNA Duplex Containing Two Consecutive Mercury-mediated Base Pairs
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6.75 | 277 | 0.08 M Potassium Chloride, 0.02 M Magnesium Chloride, 0.012 M Spermine Tetrahydrochloride, 40% 2-methyl-2,4-pentanediol, 0.04 M Sodium cacodylate trihydrate, pH 6.75, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.86 | 56.98 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 70.785 | α = 90 |
b = 70.785 | β = 90 |
c = 108.037 | γ = 120 |
Symmetry | |
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Space Group | H 3 |
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 | CCD | ADSC QUANTUM 315r | 2014-01-13 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SSRF BEAMLINE BL17U | 1.00928 | SSRF | BL17U |
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 | 2.357 | 36.01 | 97.64 | 0.084 | 0.093 | 10.1 | 16444 | 2 | 2 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Resolution (High) | Resolution (Low) | Cut-off Sigma (I) | Cut-off Sigma (F) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | R-Free Selection Details | Mean Isotropic B | ||||
X-RAY DIFFRACTION | SAD | 2.357 | 26.658 | 2 | 1.96 | 16263 | 754 | 97.64 | 0.2167 | 0.2155 | 0.23 | 0.2405 | 0.25 | RANDOM | 76.86 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 33.411 |
f_angle_d | 0.585 |
f_chiral_restr | 0.024 |
f_bond_d | 0.004 |
f_plane_restr | 0.002 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | |
Nucleic Acid Atoms | 1224 |
Solvent Atoms | 12 |
Heterogen Atoms | 6 |
Software
Software | |
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Software Name | Purpose |
HKL-2000 | data collection |
SHELXS | phasing |
PHENIX | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |