3FHG
Crystal structure of Sulfolobus solfataricus 8-oxoguanine DNA glycosylase (SsOgg)
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.5 | 285 | 50 mM sodium cacodylate, 2M (NH4)2SO4, 10mM MgSO4, (from four years old crystal tray), pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 285K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.52 | 51.15 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 110.96 | α = 90 |
b = 110.96 | β = 90 |
c = 34.41 | γ = 120 |
Symmetry | |
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Space Group | P 6 |
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 | Adjustable focus K-B pair Si plus Pt, Rh coatings | 2008-03-19 | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 23-ID-B | 0.9794 | APS | 23-ID-B |
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 | 1.9 | 20 | 95.9 | 0.085 | 0.06 | 17.6 | 5.7 | 37393 | 37358 | 24.1 |
Highest Resolution Shell | |||||||||||||||||||
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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 | 1.9 | 2 | 100 | 0.536 | 0.696 | 2.3 | 5.7 | 5344 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||
X-RAY DIFFRACTION | THROUGHOUT | PDB entry 3FHF | 1.9 | 19.7 | 37350 | 35849 | 1902 | 99.9 | 0.224 | 0.226 | 0.207 | 0.248 | RANDOM | 33.084 |
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] | |
1.84 | 1.84 | -3.69 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
c_dihedral_angle_d | 17.7 |
c_scangle_it | 3.06 |
c_scbond_it | 2.08 |
c_mcangle_it | 1.87 |
c_mcbond_it | 1.28 |
c_angle_deg | 1.1 |
c_improper_angle_d | 0.7 |
c_bond_d | 0.005 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1707 |
Nucleic Acid Atoms | |
Solvent Atoms | 116 |
Heterogen Atoms | 80 |
Software
Software | |
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Software Name | Purpose |
XSCALE | data processing |
CNS | refinement |
PDB_EXTRACT | data extraction |
Blu-Ice | data collection |
XDS | data reduction |
XSCALE | data scaling |
MOLREP | phasing |