3UYB
X-ray crystal structure of the ruthenium complex [Ru(tap)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 | 298 | 10%(v/v) 2-methyl-2,4-pentanediol, 40mM sodium cacodylate, 12mM spermine tetra-HCl, 80mM sodium chloride, 20mM barium chloride, 1mM DNA d(TCGGTACCGA), 1mM lambda-[Ru(tap)2dppz)Cl2 , pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.52 | 65.05 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 54.376 | α = 90 |
b = 54.376 | β = 90 |
c = 28.995 | 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 | PIXEL | PSI PILATUS 6M | 2011-06-12 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID29 | 0.98400 | ESRF | ID29 |
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 | 1.5 | 38.45 | 99.9 | 7382 | 1.7 | 1.7 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||||
1 | 1.5 | 1.58 | 100 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | 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 | 1.5 | 38.45 | 1.7 | 6591 | 316 | 93.76 | 0.12859 | 0.1267 | 0.16672 | RANDOM | 19.742 |
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] | |
-0.06 | -0.06 | 0.11 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_sphericity_free | 25.876 |
r_sphericity_bonded | 13.777 |
r_rigid_bond_restr | 9.612 |
r_angle_refined_deg | 3.537 |
r_chiral_restr | 0.084 |
r_gen_planes_refined | 0.038 |
r_bond_refined_d | 0.034 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | |
Nucleic Acid Atoms | 202 |
Solvent Atoms | 66 |
Heterogen Atoms | 103 |
Software
Software | |
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Software Name | Purpose |
MxCuBE | data collection |
SHELXCD | phasing |
SHELXE | model building |
REFMAC | refinement |
XDS | data reduction |
SCALA | data scaling |