5WWR
Crystal structure of human NSun6/tRNA/SFG
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION | 8.5 | 289 | 0.1 M SPG, 25% (w/v) PEG 1500, 50 mM NaF |
Crystal Properties | |
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Matthews coefficient | Solvent content |
4.18 | 70.56 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 206.908 | α = 90 |
b = 170.478 | β = 108.55 |
c = 76.999 | 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 | 100 | PIXEL | DECTRIS PILATUS3 S 6M | 2016-07-14 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SSRF BEAMLINE BL19U1 | 0.97776 | SSRF | BL19U1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 3.096 | 50 | 98.2 | 19.7 | 6.7 | 45890 | 61.73 |
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 | FREE R-VALUE | 5WWQ, 2DU3 | 3.096 | 42.892 | 1.35 | 36230 | 1793 | 78.69 | 0.1973 | 0.1953 | 0.2352 | 55.2541 |
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] | |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 13.23 |
f_angle_d | 0.593 |
f_chiral_restr | 0.024 |
f_bond_d | 0.003 |
f_plane_restr | 0.003 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 7091 |
Nucleic Acid Atoms | 3072 |
Solvent Atoms | |
Heterogen Atoms | 54 |
Software
Software | |
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Software Name | Purpose |
HKL-3000 | data collection |
HKL-3000 | data scaling |
PHENIX | refinement |
PDB_EXTRACT | data extraction |
SCALEPACK | data reduction |
PHASER | phasing |
HKL | data reduction |
SCALEPACK | data scaling |