3IAY
Ternary complex of DNA polymerase delta
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 5.5 | 293 | 12% PEG 4000, NaAc pH 5.5, 200mM CaAc., VAPOR DIFFUSION, HANGING DROP, temperature 293K |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.5 | 50.76 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 81.077 | α = 90 |
| b = 85.948 | β = 111.1 |
| c = 86.872 | 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 QUANTUM 315 | 2007-10-13 | M | SINGLE WAVELENGTH | ||||||
| 2 | 1 | x-ray | 100 | CCD | ADSC QUANTUM 210 | 2007-08-29 | M | SINGLE WAVELENGTH | ||||||
| 3 | 1 | x-ray | 100 | CCD | ADSC QUANTUM 315 | 2007-10-13 | M | MAD | ||||||
| 4 | 1 | x-ray | 100 | CCD | ADSC QUANTUM 315 | 2007-11-08 | M | SINGLE WAVELENGTH | ||||||
| 1,2,3,4 | 1 | |||||||||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | NSLS BEAMLINE X29A | NSLS | X29A | |
| 2 | SYNCHROTRON | NSLS BEAMLINE X12B | NSLS | X12B | |
| 3 | SYNCHROTRON | APS BEAMLINE 17-ID | APS | 17-ID | |
| 4 | |||||
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 | |||||||||
| 1,2,3,4 | 2 | 41.52 | 98.3 | 73557 | 69856 | 2 | 2 | ||||||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||||
| 1,2,3,4 | 2 | 2.07 | 97.9 | ||||||||||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Number Reflections (All) | 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 | MIR | THROUGHOUT | 2 | 41.52 | 73557 | 69856 | 3692 | 98.25 | 0.19497 | 0.19281 | 0.23589 | RANDOM | 28.037 | ||||||
| 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] | |
| -0.29 | 0.5 | 0.56 | 0.09 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 33.958 |
| r_dihedral_angle_4_deg | 17.191 |
| r_dihedral_angle_3_deg | 14.138 |
| r_dihedral_angle_1_deg | 5.646 |
| r_scangle_it | 2.663 |
| r_scbond_it | 1.708 |
| r_angle_refined_deg | 1.227 |
| r_mcangle_it | 1.033 |
| r_mcbond_it | 0.554 |
| r_chiral_restr | 0.081 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 6986 |
| Nucleic Acid Atoms | 569 |
| Solvent Atoms | 558 |
| Heterogen Atoms | 41 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| ADSC | data collection |
| SHARP | phasing |
| REFMAC | refinement |
| HKL-2000 | data reduction |
| HKL-2000 | data scaling |
