4R8J
d(TCGGCGCCGA) with lambda-[Ru(TAP)2(dppz)]2+ soaked in D2O
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | 6 | 291 | The drops contained 1 l of 2mM oligonuclotide, 1 l of 4mM rac [Ru(TAP)2(dppz)]Cl2 and 6 l of the following solution; 10% (vol/vol) MPD, 40 mM sodium cacodylate (pH 6.0), 12mM spermine tetra-HCl, 80mM sodium chloride and 20 mM barium chloride. The drop was equilibrated against 1ml of 35% (vol/vol) 2-methyl-2,4-pentanediol (MPD) in H2O , VAPOR DIFFUSION, SITTING DROP, temperature 291K | |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.9 | 57.65 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 42.37 | α = 90 |
| b = 42.37 | β = 90 |
| c = 39.42 | 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 | PIXEL | PSI PILATUS 6M | 2014-08-14 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | DIAMOND BEAMLINE I03 | Diamond | I03 | |
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 | 1.21 | 18.66 | 99.9 | 11471 | -3 | ||||||||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Number Reflections (All) | 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 | 1.21 | 18.66 | 11471 | 10864 | 568 | 99.9 | 0.11 | 0.109 | 0.125 | RANDOM | 22.51 | ||||||
| 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] | |
| -0.41 | -0.41 | 0.82 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_sphericity_free | 28.452 |
| r_sphericity_bonded | 14.099 |
| r_rigid_bond_restr | 5.669 |
| r_angle_other_deg | 3.753 |
| r_scangle_other | 3.408 |
| r_long_range_B_refined | 3.383 |
| r_long_range_B_other | 3.065 |
| r_angle_refined_deg | 2.592 |
| r_scbond_it | 2.514 |
| r_scbond_other | 2.51 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | |
| Nucleic Acid Atoms | 202 |
| Solvent Atoms | 73 |
| Heterogen Atoms | 53 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| GDA | data collection |
| SHELXCD | phasing |
| REFMAC | refinement |
| XDS | data reduction |
| SCALA | data scaling |
| SHELXE | model building |
