3NGD
Structural Basis for Proficient Incorporation of dTTP Opposite O6-methylguanine by Human DNA Polymerase Iota
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2ALZ | 2ALZ minus DNA |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.5 | 277 | 0.2 M ammonium sulfate, 12.5% PEG 5000 monomethylether, 0.1 M MES buffer, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.42 | 49.15 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 97.999 | α = 90 |
b = 97.999 | β = 90 |
c = 202.552 | γ = 120 |
Symmetry | |
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Space Group | P 65 2 2 |
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 | Bruker Platinum 135 | Bruker Montel Confocal Multilayer Mirrors | 2009-09-03 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | BRUKER AXS MICROSTAR | 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 | 2.8 | 80 | 96.8 | 0.174 | 11.2 | 17.9 | 14304 |
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) | |||||||||||
2.8 | 2.85 | 86.7 | 0.872 | 1.1 | 3.8 | 627 |
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 | 2ALZ minus DNA | 2.8 | 80 | 13705 | 704 | 96.89 | 0.21836 | 0.21504 | 0.28377 | RANDOM | 46.048 |
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] | |
1.03 | 0.51 | 1.03 | -1.54 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 44.534 |
r_dihedral_angle_4_deg | 21.919 |
r_dihedral_angle_3_deg | 20.725 |
r_dihedral_angle_1_deg | 6.744 |
r_scangle_it | 2.689 |
r_angle_refined_deg | 1.695 |
r_scbond_it | 1.607 |
r_mcangle_it | 0.928 |
r_mcbond_it | 0.464 |
r_chiral_restr | 0.104 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2898 |
Nucleic Acid Atoms | 309 |
Solvent Atoms | 64 |
Heterogen Atoms | 28 |
Software
Software | |
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Software Name | Purpose |
PROTEUM PLUS | data collection |
PHASER | phasing |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |