3UPU
Crystal structure of the T4 Phage SF1B Helicase Dda
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.5 | 291.1 | 4.5% w/v PEG8000, 8% v/v ethylene glycol, 0.1 M HEPES, pH 6.5, 20 mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 291.1K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.26 | 62.3 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 225.536 | α = 90 |
b = 107.253 | β = 94.128 |
c = 85.475 | γ = 90 |
Symmetry | |
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Space Group | C 1 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 | 77.2 | CCD | MARMOSAIC 300 mm CCD | 2009-06-19 | M | SINGLE WAVELENGTH | ||||||
2 | 1 | x-ray | 77.2 | CCD | MARMOSAIC 225 mm CCD | 2010-10-29 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 22-ID | 0.9793 | APS | 22-ID |
2 | SYNCHROTRON | APS BEAMLINE 22-BM | 1.0 | APS | 22-BM |
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 | 3.299 | 36.035 | 95.8 | 0.092 | 19.82 | 7.1 | 29389 | 92.36 |
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) | |||||||||||
1,2 | 3.299 | 3.42 | 71.4 | 0.473 | 2.05 | 4.5 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | 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 | SAD | 3.299 | 32.271 | 29389 | 1392 | 91.06 | 0.2065 | 0.2038 | 0.2576 | RANDOM | 110.0717 |
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] | |
0.8054 | -7.0719 | 19.6229 | -20.4283 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 18.449 |
f_angle_d | 0.916 |
f_chiral_restr | 0.061 |
f_bond_d | 0.004 |
f_plane_restr | 0.004 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 10566 |
Nucleic Acid Atoms | 471 |
Solvent Atoms | 10 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
PDB_EXTRACT | data extraction |
SERGUI | data collection |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
PHENIX | phasing |