2XCA
TERNARY COMPLEX OF SULFOLOBUS SOLFATARICUS DPO4 DNA POLYMERASE, 7,8- DIHYDRO-8-OXODEOXYGUANINE MODIFIED DNA AND dGTP - MAGNESIUM FORM
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | 7.5 | RESERVOIR: 12-20% POLYETHYLENE GLYCOL 3350, 0.2 M AMMONIUM ACETATE, 0.1 M MAGNESIUM ACETATE, 20 MM TRIS (PH 7.5) DROP: 10MM TRIS-CL PH 7.5, 30 MM NACL, 0.5MM DGTP, 2.5MM MGCL2, 6-10% POLYETHYLENE GLYCOL 3350 0.1M AMMONIUM ACETATE, 0.05M MAGNESIUM ACETATE | ||
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 3.23 | 50.09 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 94.443 | α = 90 |
| b = 103.909 | β = 90 |
| c = 52.707 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | P 21 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 | 110 | CCD | MARRESEARCH | 2007-02-05 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | APS BEAMLINE 5ID-B | APS | 5ID-B | |
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 | 2.5 | 29.13 | 99.6 | 0.06 | 21.3 | 5.8 | 18457 | 1 | 46.9 | ||||||||||
| 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 | 2.5 | 2.66 | 99.9 | 0.49 | 4.2 | 5.3 | |||||||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | 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 | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 2C22 | 2.5 | 29.13 | 18457 | 900 | 99.6 | 0.22 | 0.22 | 0.259 | RANDOM | 44.1 | ||||||
| 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] | |
| 4.73 | -0.9 | -3.82 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| c_dihedral_angle_d | 21.6 |
| c_scangle_it | 3.01 |
| c_mcangle_it | 2.24 |
| c_scbond_it | 1.93 |
| c_improper_angle_d | 1.55 |
| c_angle_deg | 1.4 |
| c_mcbond_it | 1.34 |
| c_bond_d | 0.008 |
| c_bond_d_na | |
| c_bond_d_prot | |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 2744 |
| Nucleic Acid Atoms | 608 |
| Solvent Atoms | 192 |
| Heterogen Atoms | 35 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| CNS | refinement |
| XDS | data reduction |
| XDS | data scaling |
| CNS | phasing |
