4LY2
X-ray crystal structure of the ruthenium complex [Ru(phen)2(dppz)]2+ bound to d(TCGGTACCGA)
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7 | 293 | Performed using the sitting drop vapour diffusion method, by adding 1ul (4mM) L-[Ru(phen)2(dppz)]2+ to a drop containing 1ul (1mM) d(TCGGTACCGA)2, and 8ul of a solution containing 12mM spermine, 10% 2-methyl-2,4-pentanediol, 40 mM sodium cacodylate pH 7.0, 80 mM NaCl and 20 mM BaCl2. This was equilibrated against 1 ml of 35% 2-methyl-2,4-pantanediol at room temperature, 20 C., VAPOR DIFFUSION, SITTING DROP, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.68 | 66.57 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 52.45 | α = 90 |
b = 52.45 | β = 90 |
c = 32.58 | 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 | 2012-06-10 | M | MAD |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID23-1 | 1.54980, 0.97240 | 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 | 1.76 | 52.45 | 98.8 | 4849 | 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 | MAD | THROUGHOUT | 2.1 | 37.09 | 2711 | 129 | 97.46 | 0.18968 | 0.18817 | 0.2186 | RANDOM | 39.17 |
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] | |
-0.6 | -0.6 | 1.19 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_angle_other_deg | 3.351 |
r_angle_refined_deg | 3.348 |
r_chiral_restr | 0.884 |
r_gen_planes_refined | 0.032 |
r_bond_refined_d | 0.016 |
r_bond_other_d | 0.003 |
r_gen_planes_other | 0.002 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | |
Nucleic Acid Atoms | 202 |
Solvent Atoms | 20 |
Heterogen Atoms | 103 |
Software
Software | |
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Software Name | Purpose |
MxCuBE | data collection |
SHELXS | phasing |
REFMAC | refinement |
MOSFLM | data reduction |
SCALA | data scaling |