3JXY
Bacillus cereus Alkylpurine DNA Glycosylase AlkD Bound to DNA Containing a GT Mismatch
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3JX7 | PDB 3JX7 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6.5 | 294 | 0.1 M BisTris pH 5.5, 25% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 294K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.26 | 45.69 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 38.2 | α = 90 |
b = 93.594 | β = 112.6 |
c = 48.118 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 1 |
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 | MARMOSAIC 300 mm CCD | 2007-11-11 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 21-ID-G | .97850 | APS | 21-ID-G |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 1.5 | 35.3 | 93.2 | 0.043 | 22 | 3.8 | 49763 | 46379 | 17.2 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 1.5 | 1.55 | 87.2 | 0.186 | 4.9 | 3.8 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Starting model | 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 | MOLECULAR REPLACEMENT | PDB 3JX7 | 1.5 | 28.164 | 1.42 | 46351 | 46341 | 2374 | 92.94 | 0.1326 | 0.1304 | 0.1735 | 24.2 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 19.906 |
f_angle_d | 0.986 |
f_chiral_restr | 0.066 |
f_bond_d | 0.005 |
f_plane_restr | 0.004 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1945 |
Nucleic Acid Atoms | 487 |
Solvent Atoms | 525 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
MAR345dtb | data collection |
PHASER | phasing |
PHENIX | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |