3K5M
Crystal structure of E.coli Pol II-abasic DNA-ddGTP Lt(-2, 2) ternary complex
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 293 | 20-25% PEGMME3350, 0.1 M ammonium formate, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.51 | 50.95 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 73.109 | α = 90 |
b = 95.228 | β = 90 |
c = 144.735 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 95 | IMAGE PLATE | RIGAKU RAXIS IV | 2008-01-10 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU | 1.5418 |
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 | 2.04 | 50 | 95.8 | 0.073 | 15.6 | 4.1 | 65181 | 62414 | -3 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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) | |||||||||||
2.04 | 2.11 | 98.7 | 0.5 | 3.1 | 4.2 | 6409 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 3K59 | 2.04 | 28.43 | 57663 | 1450 | 88.7 | 0.243 | 0.26 | Random | 34.132 |
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] | |
5.759 | -2.918 | -2.841 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
c_scangle_it | 2.536 |
c_mcangle_it | 1.825 |
c_scbond_it | 1.792 |
c_angle_d | 1.707 |
c_mcbond_it | 1.212 |
c_bond_d | 0.013 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 6204 |
Nucleic Acid Atoms | 663 |
Solvent Atoms | 491 |
Heterogen Atoms | 32 |
Software
Software | |
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Software Name | Purpose |
StructureStudio | data collection |
MOLREP | phasing |
CNS | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |