5DQG
Crystal Structure of Human DNA Polymerase Eta Inserting dAMPNPP Opposite O4-Ethylthymidine
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 4O3N | |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 5.5 | 291 | 0.1 M MES pH 5.5, 5mM magnesium chloride, 22% PEG 2000 MME |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.11 | 41.79 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 98.82 | α = 90 |
| b = 98.82 | β = 90 |
| c = 82.017 | γ = 120 |
| Symmetry | |
|---|---|
| Space Group | P 61 |
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 | MARMOSAIC 300 mm CCD | 2014-08-15 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | APS BEAMLINE 21-ID-G | 0.97856 | APS | 21-ID-G |
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 | 2.29 | 59.21 | 100 | 0.155 | 0.155 | 8.4 | 5.6 | 20600 | 20600 | -3 | |||||||||
| 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 | 2.29 | 2.35 | 100 | 0.595 | 3.2 | 5.6 | |||||||||||||
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 (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | R-Free Selection Details | Mean Isotropic B | ||||
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 4O3N | 2.29 | 59.21 | 19497 | 1071 | 99.99 | 0.17836 | 0.17579 | 0.18 | 0.22678 | 0.23 | RANDOM | 31.071 | ||||
| Temperature Factor Modeling | ||||||
|---|---|---|---|---|---|---|
| Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[2][2] | Anisotropic B[3][3] | |||
| -0.45 | -0.22 | -0.45 | 1.45 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 39.654 |
| r_dihedral_angle_4_deg | 17.623 |
| r_dihedral_angle_3_deg | 15.014 |
| r_long_range_B_other | 7.231 |
| r_long_range_B_refined | 7.23 |
| r_dihedral_angle_1_deg | 5.927 |
| r_scangle_other | 4.407 |
| r_mcangle_it | 3.362 |
| r_mcangle_other | 3.361 |
| r_scbond_it | 2.86 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 3366 |
| Nucleic Acid Atoms | 389 |
| Solvent Atoms | 212 |
| Heterogen Atoms | 38 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| MOSFLM | data reduction |
| SCALA | data scaling |
| PHASER | phasing |
