3I1D
Distinct recognition of three-way DNA junctions by the two enantiomers of a metallo-supramolecular cylinder ('helicate')
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6.5 | 293 | 10 mM Magnesium acetate, 50 mM Sodium cacodylate, 1.3 M Lithium sulfate , pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
4.85 | 74.65 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 74.97 | α = 90 |
b = 74.97 | β = 90 |
c = 74.97 | γ = 90 |
Symmetry | |
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Space Group | P 43 3 2 |
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 4 | 2005-03-05 | M | SINGLE WAVELENGTH | ||||||
2 | 1 | x-ray | 100 | CCD | ADSC QUANTUM 210r | 2003-05-05 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID14-4 | 0.9763 | ESRF | ID14-4 |
2 | SYNCHROTRON | ESRF BEAMLINE BM16 | 1.739 | ESRF | BM16 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge 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 | 2.5 | 18.182 | 99.6 | 0.074 | 33.5 | 15.9 | 2766 | 2766 | -3 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
2.5 | 2.6 | 100 | 0.798 | 4.08 | 13.7 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | 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 | SAD | THROUGHOUT | 2.5 | 18.18 | 2629 | 127 | 100 | 0.24546 | 0.24482 | 0.25918 | RANDOM | 55.027 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_scangle_it | 3.53 |
r_scbond_it | 2.131 |
r_angle_refined_deg | 2.083 |
r_chiral_restr | 0.11 |
r_bond_refined_d | 0.014 |
r_gen_planes_refined | 0.008 |
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 | 240 |
Solvent Atoms | 5 |
Heterogen Atoms | 267 |
Software
Software | |
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Software Name | Purpose |
MxCuBE | data collection |
SHELXCD | phasing |
SHELXE | model building |
REFMAC | refinement |
XDS | data reduction |
XSCALE | data scaling |