1OKB
crystal structure of Uracil-DNA glycosylase from Atlantic cod (Gadus morhua)
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 7.5 | 0.1M HEPES PH 7.5, 1.4M SODIUM CITRATE |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.71 | 54.7 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 68.58 | α = 90 |
b = 67.189 | β = 119.86 |
c = 68.644 | 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 | 120 | IMAGE PLATE | MAR scanner 345 mm plate | 2001-02-15 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE BM1A | ESRF | BM1A |
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 | 1.9 | 12 | 98.7 | 0.096 | 10.2 | 3.3 | 42162 | 19.45 |
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 | 1.9 | 2 | 97.5 | 0.522 | 2 | 2.9 |
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 1AKZ | 1.9 | 12 | 42162 | 2112 | 98.7 | 0.1861 | 0.1861 | 0.2057 | RANDOM | 22.4043 |
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] | |
1.623 | 2.017 | -3.129 | 1.506 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
c_dihedral_angle_d | 22.207 |
c_scangle_it | 3.184 |
c_scbond_it | 2.125 |
c_mcangle_it | 2.003 |
c_mcbond_it | 1.291 |
c_angle_deg | 1.189 |
c_improper_angle_d | 0.832 |
c_bond_d | 0.005 |
c_bond_d_na | |
c_bond_d_prot |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3574 |
Nucleic Acid Atoms | |
Solvent Atoms | 343 |
Heterogen Atoms | 14 |
Software
Software | |
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Software Name | Purpose |
CNS | refinement |
DENZO | data reduction |
SCALA | data scaling |
CNS | phasing |