6DGD
PriA helicase bound to dsDNA of a DNA replication fork
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 4NL4 | 4NL4 removing the winged helix domain |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 5.6 | 293 | 85 mM sodium citrate-NaOH pH 5.60, 0.25 M ammonium suflate, 0.75 M lithium sulfate, and 4 % glycerol |
2 | VAPOR DIFFUSION, HANGING DROP | 5.6 | 293 | 85 mM sodium citrate-NaOH pH 5.60, 0.25 M ammonium suflate, 0.8 M lithium sulfate, 4 % glycerol, 5 mM spermidine tetrahydrochloride, 20 mM praseodymium III acetate hydrate |
3 | VAPOR DIFFUSION, HANGING DROP | 5.6 | 293 | 85 mM sodium citrate-NaOH pH 5.60, 0.25 M ammonium suflate, 0.75 M lithium sulfate, 4 % glycerol, 5 mM spermidine tetrahydrochloride, and 0.1-0.2 mM adenosine diphosphate |
4 | VAPOR DIFFUSION, HANGING DROP | 5.6 | 293 | 85 mM sodium citrate-NaOH pH 5.60, 0.25 M ammonium suflate, 0.75 M lithium sulfate, 4 % glycerol, 5 mM spermidine tetrahydrochloride, and 0.1-0.2 mM potassium chloride |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 100.56 | α = 90 |
b = 106.76 | β = 90 |
c = 256.83 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
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 EIGER X 9M | 2016-11-26 | M | SINGLE WAVELENGTH | ||||||
2 | 2 | x-ray | 100 | PIXEL | DECTRIS EIGER X 9M | 2016-11-26 | M | SINGLE WAVELENGTH | ||||||
3 | 3 | x-ray | 100 | PIXEL | DECTRIS EIGER X 9M | 2016-06-25 | M | SINGLE WAVELENGTH | ||||||
4 | 4 | x-ray | 100 | PIXEL | DECTRIS EIGER X 9M | 2016-06-25 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 21-ID-D | 1.1271295 | APS | 21-ID-D |
2 | SYNCHROTRON | APS BEAMLINE 21-ID-D | 1.1271295 | APS | 21-ID-D |
3 | SYNCHROTRON | APS BEAMLINE 21-ID-D | 1.1271997 | APS | 21-ID-D |
4 | SYNCHROTRON | APS BEAMLINE 21-ID-D | 1.1271997 | APS | 21-ID-D |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | Rrim I (All) | CC (Half) | 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 | |||||||
3 | 2.81 | 49.87 | 98.5 | 0.097 | 0.999 | 16.87 | 13.4 | 66924 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Rrim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
3 | 2.81 | 2.89 | 80.6 | 3.237 | 0.458 | 0.7 | 10.7 |
Refinement
Statistics | |||||||||||||||||||
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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 | Mean Isotropic B | ||||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 4NL4 removing the winged helix domain | 2.823 | 49.343 | 66476 | 1999 | 98.81 | 0.2475 | 0.2899 |
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 | 13.636 |
f_angle_d | 1.134 |
f_chiral_restr | 0.065 |
f_bond_d | 0.013 |
f_plane_restr | 0.007 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 10577 |
Nucleic Acid Atoms | 1000 |
Solvent Atoms | 2 |
Heterogen Atoms | 69 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
XDS | data reduction |
XSCALE | data scaling |
PHASER | phasing |