6LWO
Crystal structure of human NEIL1(R242, Y244H) bound to duplex DNA containing 2'-fluoro-2'-deoxy-5,6-dihydrouridine
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 |
3.04 | 59.5 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 73.926 | α = 90 |
b = 109.447 | β = 90 |
c = 170.603 | 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 | 2017-06-25 | 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 | 2.48 | 50 | 99.7 | 0.076 | 0.084 | 0.034 | 14.1 | 5.9 | 47463 |
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 | 2.48 | 2.52 | 100 | 0.997 | 1.094 | 0.446 | 0.707 | 6.1 |
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 | 2.51 | 36.15 | 44932 | 2466 | 98.24 | 0.2048 | 0.2027 | 0.2428 | RANDOM | 75.438 |
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] | |
-0.89 | -2.15 | 3.04 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.104 |
r_dihedral_angle_4_deg | 19.9 |
r_dihedral_angle_3_deg | 16.696 |
r_dihedral_angle_1_deg | 10.663 |
r_angle_refined_deg | 1.541 |
r_angle_other_deg | 1.322 |
r_chiral_restr | 0.079 |
r_bond_refined_d | 0.009 |
r_gen_planes_refined | 0.008 |
r_bond_other_d | 0.002 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 5730 |
Nucleic Acid Atoms | 1575 |
Solvent Atoms | 277 |
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 |