X-ray crystal structure of the ruthenium complex [Ru(Tap)2(dppz-{Me2})]2+ bound to d(TCGGTACCGA)
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 7 | 293 | 10ul drop containing: 1ul of 4mM lambda-[Ru(TAP)2(dppz-{Me2})]2+; 1ul of 1mM d(TCGGTACCGA)2, and a 8ul solution containing 12mM spermine, 10% 2-methyl-2,4-pentanediol, 40mM sodium cacodylate pH 7.0, 80mM NaCl and 20mM BaCl2. This was equilibrated against a 1ml reservoir of 35% 2-methyl-2,4-pantanediol., VAPOR DIFFUSION, SITTING DROP, temperature 293K |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 3.86 | 68.17 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 52.22 | α = 90 |
| b = 52.22 | β = 90 |
| c = 34.52 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | P 43 21 2 |
Diffraction
| Diffraction Experiment | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 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 | MAD | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | ESRF BEAMLINE ID23-1 | 0.97630, 1.65310 | ESRF | ID23-1 |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 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 | 1.86 | 36.93 | 2 | ||||||||||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 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 (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | R-Free Selection Details | Mean Isotropic B | |||||
| X-RAY DIFFRACTION | THROUGHOUT | 2.05 | 36.93 | 3048 | 138 | 97.82 | 0.24806 | 0.24498 | 0.24 | 0.32103 | 0.32 | RANDOM | 44.423 | ||||||
| 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] | |
| 0.86 | 0.86 | -1.72 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_angle_other_deg | 2.923 |
| r_angle_refined_deg | 2.184 |
| r_chiral_restr | 0.151 |
| r_bond_refined_d | 0.022 |
| r_gen_planes_refined | 0.021 |
| r_gen_planes_other | 0.005 |
| r_bond_other_d | 0.003 |
| r_dihedral_angle_1_deg | |
| r_dihedral_angle_2_deg | |
| r_dihedral_angle_3_deg | |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | |
| Nucleic Acid Atoms | 193 |
| Solvent Atoms | 12 |
| Heterogen Atoms | 107 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| MxCuBE | data collection |
| SHELXS | phasing |
| REFMAC | refinement |
| MOSFLM | data reduction |
| SCALA | data scaling |
