3FLO
Crystal structure of the carboxyl-terminal domain of yeast DNA polymerase alpha in complex with its B subunit
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 6 | 291 | 0.1M MES, 1.26M Ammonium Sulfate, 3mM TCEP, pH6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 3.42 | 64.04 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 85.411 | α = 90 |
| b = 142.633 | β = 102.33 |
| c = 175.255 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | P 1 21 1 |
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 Q315R | silicon monochromator | 2007-06-16 | M | SINGLE WAVELENGTH | |||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | ESRF BEAMLINE ID29 | ESRF | ID29 | |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym 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 | 31.9 | 99.8 | 0.102 | 0.102 | 5.2 | 7.3 | 141597 | 141597 | 58.4 | |||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
| 1 | 2.5 | 2.64 | 99.7 | 0.652 | 0.652 | 1.2 | 7.4 | 20778 | |||||||||||
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 | SAD | THROUGHOUT | 2.5 | 31.9 | 134185 | 7082 | 99.8 | 0.192 | 0.191 | 0.218 | RANDOM | 43.61 | |||||||
| 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] | |
| 0.51 | -0.45 | -0.8 | 0.1 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 35.132 |
| r_dihedral_angle_4_deg | 20.359 |
| r_dihedral_angle_3_deg | 15.726 |
| r_dihedral_angle_1_deg | 6.323 |
| r_scangle_it | 2.746 |
| r_scbond_it | 2.056 |
| r_angle_refined_deg | 1.545 |
| r_mcangle_it | 1.154 |
| r_mcbond_it | 0.997 |
| r_angle_other_deg | 0.976 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 19648 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 571 |
| Heterogen Atoms | 333 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| ADSC | data collection |
| PHENIX | model building |
| REFMAC | refinement |
| MOSFLM | data reduction |
| SCALA | data scaling |
| PHENIX | phasing |
