3UXU
The structure of the catalytic domain of the Sulfolobus Spindle-shaped viral integrase reveals an evolutionarily conserved catalytic core and supports a mechanism of DNA cleavage in trans
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7 | 295 | 20% PEG 3350, 1% Tryptone, and 0.1 M HEPES at pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.48 | 64.61 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 73.963 | α = 90 |
b = 73.963 | β = 90 |
c = 176.251 | 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 | PIXEL | DECTRIS PILATUS 6M | Rh coated flat mirror | 2009-12-05 | M | SINGLE WAVELENGTH | |||||
2 | 1 | x-ray | 100 | PIXEL | DECTRIS PILATUS 6M | Rh coated flat mirror | 2009-12-05 | M | MAD |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SSRL BEAMLINE BL11-1 | 0.84917 | SSRL | BL11-1 |
2 | SYNCHROTRON | SSRL BEAMLINE BL11-1 | 0.97891, 0.91837, 0.97939 | SSRL | BL11-1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym 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 | 2.7 | 50 | 99.9 | 0.033 | 0.043 | 5.8 | 13.5 | 8414 | 10.2 | 595.3 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1,2 | 2.7 | 2.75 | 100 | 0.299 | 0.315 | 42.3 | 13.5 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation 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 | MAD | THROUGHOUT | 2.706 | 36.32 | 8310 | 7900 | 410 | 99.14 | 0.19394 | 0.19286 | 0.21442 | RANDOM | 63.971 |
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] | |
0.81 | 0.41 | 0.81 | -1.22 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 30.384 |
r_dihedral_angle_4_deg | 21.798 |
r_dihedral_angle_3_deg | 16.337 |
r_scangle_it | 6.472 |
r_dihedral_angle_1_deg | 6.429 |
r_scbond_it | 3.697 |
r_mcangle_it | 3.536 |
r_mcbond_it | 1.964 |
r_angle_refined_deg | 1.496 |
r_angle_other_deg | 0.868 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1329 |
Nucleic Acid Atoms | |
Solvent Atoms | 17 |
Heterogen Atoms | 5 |
Software
Software | |
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Software Name | Purpose |
Blu-Ice | data collection |
AutoSol | phasing |
REFMAC | refinement |
HKL-2000 | data reduction |
SCALEPACK | data scaling |