1Q8I
Crystal structure of ESCHERICHIA coli DNA Polymerase II
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 5.3 | 295 | Citrate , PEG3K, DTT, EDTA, Glycerol, pH 5.3, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
| 2 | VAPOR DIFFUSION, HANGING DROP | 5.5 | 295 | Citrate , PEG3K, DTT, EDTA, Glycerol, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
| 3 | VAPOR DIFFUSION, HANGING DROP | 5.8 | 295 | Citrate , PEG3K, DTT, MgCl2, Glycerol, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 92.383 | α = 90 |
| b = 116.596 | β = 90 |
| c = 82.43 | 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 | 100 | CCD | MARRESEARCH | M | SINGLE WAVELENGTH | |||||||
| 2 | 1 | x-ray | 100 | CCD | CUSTOM-MADE | M | SINGLE WAVELENGTH | |||||||
| 3 | 1 | x-ray | M | |||||||||||
| 1,2,3 | 1 | |||||||||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | APS BEAMLINE 5ID-B | 1.0 | APS | 5ID-B |
| 2 | SYNCHROTRON | APS BEAMLINE 5ID-B | 1.0 | APS | 5ID-B |
| 3 | SYNCHROTRON | APS BEAMLINE 19-ID | 1.77 | APS | 19-ID |
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 | |||||||||
| 1,2,3 | 2 | 29.7 | 60657 | ||||||||||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Diffraction ID | Structure Solution Method | Cross Validation method | 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 | MIRAS | THROUGHOUT | 2 | 20 | 57543 | 3064 | 99.76 | 0.19872 | 0.19672 | 0.23612 | RANDOM | 26.269 | |||||||
| 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] | |
| -1.59 | -0.64 | 2.23 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 20.633 |
| r_dihedral_angle_3_deg | 18.472 |
| r_scangle_it | 8.99 |
| r_scbond_it | 6.473 |
| r_dihedral_angle_1_deg | 4.816 |
| r_mcangle_it | 4.285 |
| r_mcbond_it | 3.171 |
| r_angle_refined_deg | 1.636 |
| r_symmetry_hbond_refined | 0.283 |
| r_nbd_refined | 0.24 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 5709 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 416 |
| Heterogen Atoms | |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| DENZO | data reduction |
| SCALEPACK | data scaling |
| MLPHARE | phasing |
