3FHF
Crystal structure of Methanocaldococcus jannaschii 8-oxoguanine DNA glycosylase (MjOgg)
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 5.9 | 285 | PEG 4000 30%, 0.1M sodium citrate, 1% b-Mercaptoethanol, pH 5.9, VAPOR DIFFUSION, HANGING DROP, temperature 285K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.21 | 44.27 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 89.44 | α = 90 |
b = 37.84 | β = 116.08 |
c = 75.01 | 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 | MARMOSAIC 300 mm CCD | Adjustable focus K-B pair Si plus Pt, Rh coatings | 2008-03-19 | M | MAD |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 23-ID-B | 0.9794, 0.9796, 0.97166 | 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 | 1.995 | 19.56 | 96.4 | 0.068 | 0.084 | 15.43 | 5.8 | 29750 | 28691 | 14.9 |
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 | 1.995 | 2.1 | 92.1 | 0.203 | 0.279 | 8.23 | 5.8 | 4041 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | 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 | 1.995 | 19.56 | 15485 | 15220 | 759 | 98.5 | 0.217 | 0.222 | 0.202 | 0.251 | RANDOM | 24.682 |
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] | |
-3.22 | 0.39 | 4.18 | -0.96 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
c_dihedral_angle_d | 18.2 |
c_scangle_it | 3.42 |
c_scbond_it | 2.33 |
c_mcangle_it | 1.89 |
c_mcbond_it | 1.31 |
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 | 1815 |
Nucleic Acid Atoms | |
Solvent Atoms | 153 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
SCALA | data processing |
CNS | refinement |
PDB_EXTRACT | data extraction |
Blu-Ice | data collection |
XDS | data reduction |
SCALA | data scaling |
SHARP | phasing |