2YG9
Structure of an unusual 3-Methyladenine DNA Glycosylase II (Alka) from Deinococcus radiodurans
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2YG8 | PDB ENTRY 2YG8 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 1 UL DROPS OF 10 MG/ML PROTEIN MIXED WITH A SOLUTION CONTAINING 1 M LICL2, 0.1 M MES PH 6.0 AND 10% PEG6000 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.44 | 49.6 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 108.311 | α = 90 |
b = 51.372 | β = 99.71 |
c = 90.039 | 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 | ADSC CCD | MIRROR | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID14-1 | ESRF | ID14-1 |
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 | 1.95 | 42.68 | 99.8 | 0.14 | 8.8 | 4.1 | 35790 | 12.76 |
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 | 1.95 | 2.06 | 99.8 | 0.48 | 3 | 4.2 |
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 2YG8 | 1.95 | 42.68 | 33988 | 1802 | 99.77 | 0.17315 | 0.17011 | 0.23101 | RANDOM | 9.348 |
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] | |
0.01 | 0.03 | -0.04 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 38.507 |
r_dihedral_angle_4_deg | 16.673 |
r_dihedral_angle_3_deg | 14.195 |
r_dihedral_angle_1_deg | 4.817 |
r_scangle_it | 3.528 |
r_scbond_it | 2.343 |
r_angle_refined_deg | 1.476 |
r_mcangle_it | 1.28 |
r_angle_other_deg | 1.017 |
r_mcbond_it | 1.013 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3073 |
Nucleic Acid Atoms | |
Solvent Atoms | 612 |
Heterogen Atoms | 12 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
MOSFLM | data reduction |
SCALA | data scaling |
MOLREP | phasing |