3U38
Intercalation of lambda-[Ru(phen)2(dppz)]2+ into d(CCGGTACCGG)2
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 7 | 298 | 40mM pH 7 sodium cacodylate, 12mM spermine, 20mM BaCl2, 10% 2-methyl-2,4-pentanediol, 1mM oligonuclotide, 3mM lambda-[Ru(phenanthroline)2dipyridophenazine]Cl2, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 3.68 | 66.54 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 52.56 | α = 90 |
| b = 52.56 | β = 90 |
| c = 32.43 | 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 | 2011-09-19 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | DIAMOND BEAMLINE I04 | 0.9464 | Diamond | I04 |
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 | 2.1 | 52.55 | 95.7 | 2908 | 2783 | 2.5 | 1 | ||||||||||||
| 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 | 2.1 | 2.16 | 100 | ||||||||||||||||
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 (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | R-Free Selection Details | Mean Isotropic B | ||||
| X-RAY DIFFRACTION | SAD | THROUGHOUT | 2.13 | 14.86 | 2764 | 2610 | 126 | 98.59 | 0.17879 | 0.17623 | 0.17 | 0.23152 | 0.24 | RANDOM | 40.415 | ||||
| Temperature Factor Modeling | ||||||
|---|---|---|---|---|---|---|
| Anisotropic B[1][1] | Anisotropic B[2][2] | Anisotropic B[3][3] | ||||
| 0.02 | 0.02 | -0.05 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_angle_refined_deg | 2.972 |
| r_chiral_restr | 0.086 |
| r_gen_planes_refined | 0.021 |
| r_bond_refined_d | 0.012 |
| r_bond_other_d | |
| r_angle_other_deg | |
| r_dihedral_angle_1_deg | |
| r_dihedral_angle_2_deg | |
| r_dihedral_angle_3_deg | |
| r_dihedral_angle_4_deg | |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | |
| Nucleic Acid Atoms | 202 |
| Solvent Atoms | 19 |
| Heterogen Atoms | 103 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
