4M3I
X-ray crystal structure of the ruthenium complex [Ru(TAP)2(dppz-{Me2})]2+ bound to d(CCGGTACCGG)
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7 | 293 | 10ul drop containing 1ul of 4mM-[Ru(TAP)2(dppz-{Me2})]2+, 1ul of 1 mM d(CCGGTACCGG)2, and a 8ul addition containing 12mM spermine, 10% 2-methyl-2,4-pentanediol, 40mM sodium cacodylate pH 7.0, 80mM NaCl and 20mM BaCl2. This was equilibrated against 1ml of 35% 2-methyl-,4-pantanediol. , VAPOR DIFFUSION, SITTING DROP, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.93 | 68.68 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 53.279 | α = 90 |
b = 53.279 | β = 90 |
c = 33.709 | γ = 90 |
Symmetry | |
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Space Group | P 43 21 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 315r | 2012-07-10 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID23-1 | 1.03320 | ESRF | ID23-1 |
Data Collection
Overall | |||||||||||||||||||
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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 | 2.1 | 53.28 | 3114 | 2 |
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 | 2.1 | 37.67 | 2774 | 129 | 93.89 | 0.25266 | 0.25147 | 0.27743 | RANDOM | 53.991 |
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] | |
2.73 | 2.73 | -5.46 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_angle_other_deg | 2.68 |
r_angle_refined_deg | 1.939 |
r_chiral_restr | 0.149 |
r_gen_planes_refined | 0.021 |
r_gen_planes_other | 0.021 |
r_bond_refined_d | 0.019 |
r_bond_other_d | 0.008 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | |
Nucleic Acid Atoms | 198 |
Solvent Atoms | 13 |
Heterogen Atoms | 107 |
Software
Software | |
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Software Name | Purpose |
MxCuBE | data collection |
SHELXS | phasing |
REFMAC | refinement |
MOSFLM | data reduction |
SCALA | data scaling |