7LXJ
Bacillus cereus DNA glycosylase AlkD bound to a duocarmycin SA-adenine nucleobase adduct and DNA containing an abasic site
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7 | 294 | 24% (w/v) PEG 8000, 50 mM HEPES pH 7.0, and 50 mM calcium chloride |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.27 | 45.87 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 124.715 | α = 90 |
b = 55.661 | β = 112.2 |
c = 47.991 | γ = 90 |
Symmetry | |
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Space Group | C 1 2 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 | RAYONIX MX-300 | 2018-10-08 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 21-ID-F | 0.97872 | APS | 21-ID-F |
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 | 1.93 | 50 | 99.9 | 0.067 | 0.073 | 0.028 | 10.9 | 6.3 | 22584 |
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 | 1.94 | 2.01 | 98.8 | 0.598 | 0.654 | 0.259 | 0.836 | 5.9 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | 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 | 3BVS | 1.93 | 44.434 | 1.35 | 22575 | 1132 | 97.99 | 0.1564 | 0.1539 | 0.2012 | RANDOM | 45.5047 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 20.811 |
f_angle_d | 1.116 |
f_chiral_restr | 0.059 |
f_bond_d | 0.011 |
f_plane_restr | 0.008 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1923 |
Nucleic Acid Atoms | 354 |
Solvent Atoms | 189 |
Heterogen Atoms | 75 |
Software
Software | |
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Software Name | Purpose |
HKL-2000 | data reduction |
DENZO | data reduction |
HKL-2000 | data scaling |
SCALEPACK | data scaling |
PHENIX | phasing |
PHASER | phasing |
Coot | model building |
PHENIX | refinement |
PDB_EXTRACT | data extraction |