6LWH
Crystal structure of human NEIL1(P2G, E3Q, K242) bound to duplex DNA containing dihydrothymine (DHT)
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 5ITY |
Crystallization
Crystalization Experiments | ||||
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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 | |
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Matthews coefficient | Solvent content |
2.73 | 54.99 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 73.593 | α = 90 |
b = 109.014 | β = 90 |
c = 168.053 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
Diffraction
Diffraction Experiment | ||||||||||||||
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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 | 2017-03-28 | 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 | |||||||||||||||||||
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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 | 2.78 | 50 | 99.9 | 0.089 | 0.097 | 0.037 | 4.2 | 6.6 | 34947 |
Highest Resolution Shell | |||||||||||||||||||
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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 | 2.78 | 2.83 | 100 | 0.629 | 0.68 | 0.257 | 0.869 | 6.8 |
Refinement
Statistics | |||||||||||||||||||
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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 | 2.78 | 49.41 | 33122 | 1766 | 99.81 | 0.2025 | 0.2004 | 0.2422 | RANDOM | 80.261 |
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] | |
-4.28 | -1.13 | 5.42 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.366 |
r_dihedral_angle_4_deg | 23.259 |
r_dihedral_angle_3_deg | 17.262 |
r_dihedral_angle_1_deg | 12.152 |
r_angle_refined_deg | 1.627 |
r_angle_other_deg | 1.374 |
r_chiral_restr | 0.078 |
r_bond_refined_d | 0.009 |
r_gen_planes_refined | 0.008 |
r_gen_planes_other | 0.003 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 5781 |
Nucleic Acid Atoms | 1575 |
Solvent Atoms | 153 |
Heterogen Atoms | 6 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
HKL-2000 | data reduction |
SCALEPACK | data scaling |
PHASER | phasing |