A: R-SwaI protein B: R-SwaI protein C: R-SwaI protein D: R-SwaI protein H: DNA (26-MER) I: DNA (26-MER) J: DNA (26-MER) K: DNA (26-MER) hetero molecules
Mass: 18.015 Da / Num. of mol.: 212 / Source method: isolated from a natural source / Formula: H2O
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Details
Compound details
The DNA strands are partially cleaved, thus the alternate conformations: A conformer (cleaved) and ...The DNA strands are partially cleaved, thus the alternate conformations: A conformer (cleaved) and B conformer (uncleaved)
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Experimental details
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Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
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Sample preparation
Crystal
Density Matthews: 2.28 Å3/Da / Density % sol: 45.98 %
Crystal grow
Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 24 - 28% PEG1000, 100 mM TrisHCl, 5 mM CaCl2, / PH range: 8 - 8.5
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Data collection
Diffraction
Mean temperature: 100 K
Diffraction source
Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.9794 Å
Monochromator: Si (111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.9794 Å / Relative weight: 1
Reflection
Resolution: 2.1→50 Å / Num. obs: 53972 / % possible obs: 96.1 % / Observed criterion σ(I): 1 / Redundancy: 6.4 % / Biso Wilson estimate: 30.46 Å2 / Rmerge(I) obs: 0.127 / Rsym value: 0.127 / Net I/σ(I): 12.5
Reflection shell
Resolution: 2.29→2.37 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.851 / Mean I/σ(I) obs: 1.1 / CC1/2: 0.613 / % possible all: 79.9
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Processing
Software
Name
Version
Classification
REFMAC
5.8.0124
refinement
HKL-2000
datareduction
HKL-2000
datascaling
PHASER
phasing
Refinement
Method to determine structure: MAD / Resolution: 2.3→49 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.936 / SU B: 20.475 / SU ML: 0.233 / Cross valid method: THROUGHOUT / ESU R: 0.408 / ESU R Free: 0.249 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.24197
2971
5.2 %
RANDOM
Rwork
0.19767
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obs
0.19992
53972
95.21 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å