DIRECT OBSERVATION OF TWO BASE-PAIRING MODES OF A CYTOSINE-THYMINE ANALOGUE WITH GUANINE IN A DNA Z-FORM DUPLEX: SIGNIFICANCE FOR BASE ANALOGUE MUTAGENESIS
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 1DCG | ZDF002 |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION | 6.5 | 277 | pH 6.50, VAPOR DIFFUSION, temperature 277.00K |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 1.65 | 25.44 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 18.23 | α = 90 |
| b = 30.63 | β = 90 |
| c = 43.78 | 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 | 292 | DIFFRACTOMETER | RIGAKU AFC-5R | |||||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | ROTATING ANODE | RIGAKU RU200 | |||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Diffraction ID | Structure Solution Method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work (Depositor) | R-Work (DCC) | R-Free (Depositor) | Mean Isotropic B | ||||||
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | ZDF002 | 1.7 | 8 | 4 | 2798 | 100 | 0.179 | 0.19 | ||||||||||
| 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 |
| n_phos_bond_it | 10.38 |
| n_phos_angle_it | 7.71 |
| n_sugar_angle_it | 5.74 |
| n_sugar_bond_it | 4.79 |
| n_multtor_nbd | 0.278 |
| n_singtor_nbd | 0.145 |
| n_chiral_restr | 0.138 |
| n_sugar_bond_angle_d | 0.076 |
| n_phos_bond_d | 0.071 |
| n_phos_bond_angle_d | 0.048 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | |
| Nucleic Acid Atoms | 240 |
| Solvent Atoms | 51 |
| Heterogen Atoms | 6 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| MERLOT | phasing |
| NUCLSQ | refinement |
