3NO0
Aquifex aeolicus type IIA topoisomerase C-terminal domain
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.5 | 291 | 50 mM NaCL, 10mM Tris-HCl pH 7.5, 225 mM NH4NO3, 20% PEG 3500, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
2 | VAPOR DIFFUSION, HANGING DROP | 7.5 | 291 | 50 mM NaCL, 10mM Tris-HCl pH 7.5, 50mM NaNO3, 20% PEG 3500, 10mM K2Pt(CN4), VAPOR DIFFUSION, HANGING DROP, temperature 291K |
3 | VAPOR DIFFUSION, HANGING DROP | 7.5 | 291 | 50 mM NaCL, 10mM Tris-HCl pH 7.5, 50mM NaNO3, 20% PEG 3500, 10 mM K2PtCl4, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
4 | VAPOR DIFFUSION, HANGING DROP | 7.5 | 291 | 50 mM NaCL, 10mM Tris-HCl pH 7.5, 50mM NaNO3, 20% PEG 3500, 10 mM NaWO4, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 43.513 | α = 91.57 |
b = 49.624 | β = 99.75 |
c = 120.35 | γ = 113.48 |
Symmetry | |
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Space Group | P 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 QUANTUM 315r | 2007-04-20 | M | SINGLE WAVELENGTH | ||||||
2 | 1 | x-ray | 100 | CCD | ADSC QUANTUM 315r | 2007-05-09 | M | SINGLE WAVELENGTH | ||||||
3 | 1 | x-ray | 100 | CCD | ADSC QUANTUM 315r | 2007-05-09 | M | SINGLE WAVELENGTH | ||||||
4 | 1 | x-ray | 100 | CCD | ADSC QUANTUM 315r | 2007-05-09 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ALS BEAMLINE 8.3.1 | 1.1 | ALS | 8.3.1 |
2 | SYNCHROTRON | ALS BEAMLINE 8.3.1 | 1.071 | ALS | 8.3.1 |
3 | SYNCHROTRON | ALS BEAMLINE 8.3.1 | 1.071 | ALS | 8.3.1 |
4 | SYNCHROTRON | ALS BEAMLINE 8.3.1 | 1.214 | ALS | 8.3.1 |
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 | ||||||||
1,2,3,4 | 1.3 | 40.851 | 93.6 | 0.031 | 28.2 | 3.4 | 222500 | 208073 | -3 | 15.36 |
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) | |||||||||||
1.3 | 1.315 | 84.8 | 0.357 | 2.4 | 2.5 | 18736 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Resolution (High) | Resolution (Low) | Number Reflections (All) | 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 | MIRAS | 1.3004 | 40.851 | 222500 | 208073 | 10451 | 93.51 | 0.1734 | 0.1725 | 0.1894 | random, 5% |
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] | |
-0.4513 | 1.3291 | 0.0436 | 1.8789 | -1.5534 | -1.4276 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 15.415 |
f_angle_d | 1.501 |
f_chiral_restr | 0.089 |
f_bond_d | 0.014 |
f_plane_restr | 0.008 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 6489 |
Nucleic Acid Atoms | |
Solvent Atoms | 948 |
Heterogen Atoms | 70 |
Software
Software | |
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Software Name | Purpose |
HKL-2000 | data collection |
SOLVE | phasing |
PHENIX | refinement |
HKL-2000 | data reduction |
SCALA | data scaling |