2OKS
X-ray Structure of a DNA Repair Substrate Containing an Alkyl Interstrand Crosslink at 1.65 Resolution
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 8 | The purified crosslinked DNA was dissolved in a buffer containing 22 mM ammonium acetate, 11 mM tris-hydroxymethyl-aminomethane (Tris)-HCl pH 8.0, and 11 mM calcium acetate. Crystals were grown using the sitting drop vapor diffusion method at 277K, in which 3 uL of a reservoir solution containing 27% 2-3 methyl-pentadiol, 115 mM calcium acetate, and 10 mM Tris-HCl pH 8.0 was added to an equal volume of DNA solution, and the mixture was equilibrated against 700 uL of the reservoir solution. Crystals first appeared after two weeks. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.95 | 37.04 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 31.87 | α = 90 |
b = 24.89 | β = 114.5 |
c = 34.35 | γ = 90 |
Symmetry | |
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Space Group | C 1 2 1 |
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 | 200 | IMAGE PLATE | RIGAKU RAXIS IV | 2004-08-01 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 1.65 | 40 | 96.1 | 0.046 | 38.1 | 4.1 | 3043 | 2924 | 8 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 1.65 | 1.71 | 79.4 | 0.047 | 25.7 | 2.56 | 239 |
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-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | FOURIER SYNTHESIS | THROUGHOUT | PDB ENTRY 1EN8 | 1.65 | 18.89 | 3043 | 2924 | 162 | 96.1 | 0.182 | 0.208 | RANDOM | 12.8 |
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] | |
-0.86 | 0.75 | 0.62 | 0.24 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
c_dihedral_angle_d | 21.3 |
c_improper_angle_d | 2.14 |
c_mcangle_it | 1.89 |
c_mcbond_it | 1.34 |
c_angle_deg | 1.1 |
c_bond_d | 0.012 |
c_scbond_it | |
c_scangle_it |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | |
Nucleic Acid Atoms | 203 |
Solvent Atoms | 75 |
Heterogen Atoms | 3 |
Software
Software | |
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Software Name | Purpose |
CNS | refinement |
CBASS | data collection |
DENZO | data reduction |
SCALEPACK | data scaling |
CNS | phasing |