4L24
Crystal structure of metallo-DNA duplex containing consecutive T-Hg(II)-T base pairs
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 1BNA |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7 | 277 | Sodium Cacodylate, Spermine tetrahydrochloride, 2-methyl-2,4-pentanediol, ammonium chloride, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.32 | 47.07 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 25.5 | α = 90 |
b = 41.27 | β = 90 |
c = 64.56 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | 2011-10-16 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | PHOTON FACTORY BEAMLINE BL-1A | 1.0 | Photon Factory | BL-1A |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 2.7 | 34.8 | 2064 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Work | R-Free | Mean Isotropic B | |||||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | 1BNA | 2.7 | 34.77 | 2064 | 187 | 99.2 | 0.258 | 0.267 | 62.5829 |
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] | |
-1.457 | 37.106 | -35.65 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
c_scbond_it | 21.154 |
c_scangle_it | 20.381 |
c_mcangle_it | 20.215 |
c_angle_deg | 1.16 |
c_bond_d | 0.006 |
c_mcbond_it |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | |
Nucleic Acid Atoms | 484 |
Solvent Atoms | 14 |
Heterogen Atoms | 2 |
Software
Software | |
---|---|
Software Name | Purpose |
CNS | refinement |
PDB_EXTRACT | data extraction |
CrystalClear | data reduction |
CrystalClear | data scaling |
PHENIX | phasing |