3M8S
Crystal structure of the large fragment of DNA polymerase I from Thermus aquaticus in a closed ternary complex with trapped 4'-methylated dTTP
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3KTQ | PDB entry 3KTQ |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6.5 | 291 | 30% (w/v) PEG 8000, 0.2M ammonium acetate, 0.02M magnesium acetate, 0.05M sodium cacodylate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.23 | 44.81 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 108.742 | α = 90 |
b = 108.742 | β = 90 |
c = 90.755 | γ = 120 |
Symmetry | |
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Space Group | P 31 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 | PIXEL | PSI PILATUS 6M | This noise-free counting device combines extraordinary spatial resolution with full frame read-out times of 5 ms. These features make it an ideal detector for PX and enable novel data acquisition modes such as continuos data acquisition and fine-phi-slicing. | 2009-05-23 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SLS BEAMLINE X06SA | 1.0000 | SLS | X06SA |
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 | 2.2 | 47.1 | 99.8 | 0.115 | 12.9 | 9.76 | 31955 | 32046 | -3 | 52.151 |
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) | |||||||||||
2.2 | 2.33 | 98.3 | 0.01052 | 1.94 | 9.25 | 5132 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | PDB entry 3KTQ | 2.2 | 47.093 | 2.01 | 27918 | 31860 | 1600 | 99.98 | 0.173 | 0.1703 | 0.2236 | 42.39 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 19.36 |
f_angle_d | 0.97 |
f_chiral_restr | 0.062 |
f_bond_d | 0.012 |
f_plane_restr | 0.003 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4283 |
Nucleic Acid Atoms | 569 |
Solvent Atoms | 122 |
Heterogen Atoms | 83 |
Software
Software | |
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Software Name | Purpose |
PHENIX | model building |
PHENIX | refinement |
XDS | data reduction |
XDS | data scaling |
PHENIX | phasing |