3KHC
Crystal Structure of Escherichia coli AlkB in complex with ssDNA containing a 1-methylguanine lesion
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2FD8 | PDB ENTRY 2FD8 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6 | 288 | 10-20% PEG 8000, 0.1M MES, 0.1M sodium chloride, 0.1M magnesium chloride, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 288K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.15 | 42.75 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 147.809 | α = 90 |
b = 41.441 | β = 120.98 |
c = 85.622 | 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 | RIGAKU SATURN 92 | 2009-05-12 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU MICROMAX-007 | 1.54 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge 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 | 2.2 | 42.69 | 99.6 | 0.104 | 9.4 | 6.94 | 22909 | 21726 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 2.2 | 2.23 | 99.94 | 0.396 | 9.4 | 6.27 | 1661 |
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 | PDB ENTRY 2FD8 | 2.2 | 23.74 | 21726 | 1156 | 99.68 | 0.21434 | 0.21126 | 0.27326 | RANDOM | 18.165 |
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] | |
-0.19 | 0.15 | -0.13 | 0.48 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.975 |
r_dihedral_angle_4_deg | 17.682 |
r_dihedral_angle_3_deg | 16.879 |
r_dihedral_angle_1_deg | 6.632 |
r_scangle_it | 1.998 |
r_angle_refined_deg | 1.619 |
r_scbond_it | 1.191 |
r_mcangle_it | 0.734 |
r_mcbond_it | 0.396 |
r_chiral_restr | 0.087 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3243 |
Nucleic Acid Atoms | 246 |
Solvent Atoms | 269 |
Heterogen Atoms | 22 |
Software
Software | |
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Software Name | Purpose |
CrystalClear | data collection |
PHASER | phasing |
REFMAC | refinement |
d*TREK | data reduction |
d*TREK | data scaling |