5MFX
Zika NS3 helicase:RNA complex
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6.5 | 293 | 20% (w/v) ethylene glycol, 10% (w/v) polyethylene glycol 8000, 0.1 M MES/Imidazole pH 6.5, 20mM sodium formate, 20mM ammonium acetate, 20mM tri-sodium citrate, 20mM sodium potassium L-tartrate. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.22 | 44.56 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 52.355 | α = 90 |
b = 73.037 | β = 93.97 |
c = 58.696 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 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 | PIXEL | DECTRIS PILATUS3 6M | 2016-09-30 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I03 | 0.976300 | Diamond | I03 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge 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 | 1.598 | 45.69 | 98.8 | 0.04 | 0.999 | 14.95 | 3 | 57739 | -3 | 31.266 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 1.598 | 1.64 | 96.2 | 0.756 | 0.484 | 1.46 | 2.86 |
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-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 2JLQ | 1.598 | 45.69 | 54856 | 2878 | 98.82 | 0.1634 | 0.1619 | 0.1914 | RANDOM | 26.389 |
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] | |
0.08 | -0.26 | -0.3 | 0.24 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.403 |
r_dihedral_angle_4_deg | 12.545 |
r_dihedral_angle_3_deg | 11.787 |
r_dihedral_angle_1_deg | 5.849 |
r_mcangle_it | 2.573 |
r_mcbond_it | 1.662 |
r_mcbond_other | 1.637 |
r_angle_refined_deg | 1.545 |
r_angle_other_deg | 0.978 |
r_chiral_restr | 0.095 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3333 |
Nucleic Acid Atoms | 92 |
Solvent Atoms | 387 |
Heterogen Atoms | 17 |
Software
Software | |
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Software Name | Purpose |
XDS | data reduction |
XSCALE | data scaling |
PHASER | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
XSCALE | data reduction |
XDS | data scaling |