2I2I
Crystal structure of the DB293-D(CGCGAATTCGCG)2 complex.
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | 7 | 293 | MAGNESIUM CHLORIDE, DNA DODECAMER, MPD, COMPOUND DB 293, SODIUM CACODYLATE BUFFER., pH 7.0, VAPOR DIFFUSION, HANGING DROP, pH 7.00 | |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.07 | 40.48 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 24.176 | α = 90 |
| b = 39.762 | β = 90 |
| c = 65.75 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | P 21 21 21 |
Diffraction
| Diffraction Experiment | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
| 1 | 1 | x-ray | 105 | IMAGE PLATE | RIGAKU RAXIS IV | OSMIC FOCUSING MIRROR SYSTEM | 2006-08-07 | M | SINGLE WAVELENGTH | |||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | ROTATING ANODE | RIGAKU RU200 | |||
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (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 | 1.63 | 25.34 | 98.6 | 0.032 | 16 | 3.36 | 8262 | 3 | |||||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
| 1.63 | 1.69 | 99.5 | 0.249 | 3.7 | 3.2 | ||||||||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (All) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | DNA PART OF NDB ENTRY GDL009 OR PDB ENTRY 2DBE. | 1.63 | 8 | 2 | 8184 | 799 | 89 | 0.228 | 0.22 | 0.313 | RANDOM | ||||||
| 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] | |
| Coordinate Error | ||
|---|---|---|
| Structure Solution Method | Refinement High Resolution | Refinement Low Resolution |
| 594 | ||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| s_similar_adp_cmpnt | 0.063 |
| s_angle_d | 0.028 |
| s_from_restr_planes | 0.015 |
| s_anti_bump_dis_restr | 0.009 |
| s_bond_d | 0.008 |
| s_non_zero_chiral_vol | 0.007 |
| s_similar_dist | |
| s_zero_chiral_vol | |
| s_rigid_bond_adp_cmpnt | |
| s_approx_iso_adps | |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | |
| Nucleic Acid Atoms | 486 |
| Solvent Atoms | 75 |
| Heterogen Atoms | 33 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| SHELXL-97 | refinement |
| CNS | refinement |
| CrystalClear | data collection |
| d*TREK | data reduction |
| d*TREK | data scaling |
| CNS | phasing |
