X-ray crystal structure of the ruthenium complex [Ru(tap)2(dppz)]2+ bound to d(TCGGCGCCGA) at medium resolution
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 6 | 277 | 10% MPD, 40mM Sodium cacodylate, 12mM Spermine hydrochloride, 80mM Sodium chloride, 20mM Barium chloride, pH 6, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.88 | 57.34 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 42.239 | α = 90 |
| b = 42.239 | β = 90 |
| c = 39.379 | 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 | 180 | CCD | OXFORD SAPPHIRE CCD | 2011-01-13 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SEALED TUBE | OXFORD DIFFRACTION ENHANCE ULTRA | 1.5418 | ||
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 | 1.723 | 29.87 | 44.02 | 5674 | 3309 | 3 | 3 | ||||||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||||
| 1 | 1.72 | 1.88 | 38.6 | ||||||||||||||||
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 | SAD | THROUGHOUT | 1.73 | 13.963 | 2497 | 147 | 86.21 | 0.1844 | 0.18214 | 0.2 | 0.23313 | 0.24 | RANDOM | 21.682 | |||||
| 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 | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_scangle_it | 3.75 |
| r_scbond_it | 2.925 |
| r_angle_refined_deg | 2.722 |
| r_chiral_restr | 0.141 |
| r_gen_planes_refined | 0.022 |
| r_bond_refined_d | 0.021 |
| r_bond_other_d | |
| r_angle_other_deg | |
| r_dihedral_angle_1_deg | |
| r_dihedral_angle_2_deg | |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | |
| Nucleic Acid Atoms | 202 |
| Solvent Atoms | 87 |
| Heterogen Atoms | 52 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| CrysalisPro | data collection |
| SHELXCD | phasing |
| SHELXE | model building |
| REFMAC | refinement |
| CrysalisPro | data reduction |
| CrysalisPro | data scaling |
