6IZX
The RNA-dependent RNA polymerase domain of dengue 2 NS5, bound with RK-0404678
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 293 | 1.6 M ammonium sulfate, 100 mM MES-NaOH (pH 6.2-6.5), and 10 mM CoCl2 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.65 | 66.32 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 236.5 | α = 90 |
b = 236.5 | β = 90 |
c = 236.5 | γ = 90 |
Symmetry | |
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Space Group | I 4 3 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 | CCD | MARMOSAIC 225 mm CCD | 2016-09-30 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SPRING-8 BEAMLINE BL26B2 | 1 | SPring-8 | BL26B2 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Sym I (Observed) | 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 | |||||||
1 | 2.43 | 77.2 | 100 | 0.205 | 0.998 | 16.36 | 22.3 | 42503 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R-Sym I (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 2.43 | 2.49 | 2.2895 | 0.601 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 2J7U | 2.43 | 55.744 | 1.34 | 42496 | 2125 | 99.98 | 0.1984 | 0.1967 | 0.2306 | 50.5695 |
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 | 5.004 |
f_angle_d | 0.899 |
f_chiral_restr | 0.05 |
f_bond_d | 0.008 |
f_plane_restr | 0.005 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4730 |
Nucleic Acid Atoms | |
Solvent Atoms | 207 |
Heterogen Atoms | 39 |
Software
Software | |
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Software Name | Purpose |
xia2 | data scaling |
PHENIX | refinement |
Coot | model building |
xia2 | data reduction |
PHENIX | phasing |