6LWL
Crystal structure of human NEIL1(R242) bound to duplex DNA containing 2'-fluoro-2'-deoxy-5,6-dihydrouridine
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 6.5 | 277.15 | 0.1 M cacodylic acid (pH 6.5), 0.1 M NaCl, 0.05 M MgCl2 and 18% (w/v) PEG 8000 |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.77 | 55.53 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 73.772 | α = 90 |
| b = 108.653 | β = 90 |
| c = 170.583 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | P 21 21 21 |
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 | MAR CCD 130 mm | 2015-12-22 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | SSRF BEAMLINE BL17U1 | 0.9793 | SSRF | BL17U1 |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | 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 | 2.54 | 50 | 99.8 | 0.084 | 0.093 | 0.037 | 10.2 | 6.1 | 45933 | ||||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
| 1 | 2.55 | 2.59 | 100 | 0.967 | 1.055 | 0.416 | 0.707 | 6.3 | |||||||||||
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 | 5ITY | 2.55 | 36.08 | 43557 | 2310 | 99.32 | 0.2113 | 0.2091 | 0.2525 | RANDOM | 80.307 | ||||||
| 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] | |
| -1.01 | -0.17 | 1.18 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 32.295 |
| r_dihedral_angle_4_deg | 21.954 |
| r_dihedral_angle_3_deg | 16.701 |
| r_dihedral_angle_1_deg | 12.069 |
| r_angle_refined_deg | 1.583 |
| r_angle_other_deg | 1.354 |
| r_chiral_restr | 0.08 |
| r_bond_refined_d | 0.01 |
| r_gen_planes_refined | 0.008 |
| r_bond_other_d | 0.003 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 5916 |
| Nucleic Acid Atoms | 1575 |
| Solvent Atoms | 222 |
| Heterogen Atoms | 6 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| PDB_EXTRACT | data extraction |
| HKL-2000 | data reduction |
| SCALEPACK | data scaling |
| PHASER | phasing |
