3VNN
Crystal Structure of a sub-domain of the nucleotidyltransferase (adenylation) domain of human DNA ligase IV
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 5.6 | 291 | 7.5% PEG 6000, 100mM MES, 0.01mg/ml papain, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.33 | 47.15 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 39.086 | α = 90 |
b = 39.086 | β = 90 |
c = 197.393 | γ = 90 |
Symmetry | |
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Space Group | P 41 2 2 |
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 | ADSC QUANTUM 315 | 2010-03-15 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID14-1 | 0.9765 | ESRF | ID14-1 |
Data Collection
Overall | |||||||||||||||||||
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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 | 2.9 | 100 | 98.8 | 0.063 | 0.063 | 15.3 | 11.9 | 3907 | 3860 | 2.5 | 89.06 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 2.9 | 2.97 | 100 | 0.544 | 0.544 | 5.19 | 11.7 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | SAD | 2.903 | 30.64 | 1.33 | 2263 | 3811 | 381 | 98.88 | 0.2767 | 0.2733 | 0.3049 | 109.8132 |
Temperature Factor Modeling | ||||||
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
8.8971 | 8.8971 | -17.7942 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 18.975 |
f_angle_d | 1.971 |
f_chiral_restr | 0.156 |
f_bond_d | 0.014 |
f_plane_restr | 0.011 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 949 |
Nucleic Acid Atoms | |
Solvent Atoms | 3 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
MxCuBE | data collection |
SOLVE | phasing |
PHENIX | refinement |
DENZO | data reduction |
SCALEPACK | data scaling |