6I8H
Structure of the plant immune signaling node EDS1 (enhanced disease susceptibility 1) in complex with nanobody ENB15
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 4NFU |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6.5 | 277.15 | Reservoir composition: 12.5 % (v/v) (RS)-2-methyl-2,4-pentanediol, 12.5 % (w/v) PEG 1000, 12.5 % (w/v) PEG3350, 0.03 M magnesium chloride, 0.03 M calcium chloride, 0.0612 M MES, 0.0388 M imidazole, pH 6.5; protein stock solution: 4.1 mg/ml protein, 50 mM sodium chloride, 1 % (v/v) glycerole, 1 mM DTT, 50 mM HEPES, pH 8.0; drop composition: 150 nl protein stock solution plus 225 nl reservoir solution; cryo conditions: the crystals were flash frozen directly from the equilibrated crystallization drops. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.66 | 53.8 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 145.887 | α = 90 |
b = 145.887 | β = 90 |
c = 152.77 | γ = 120 |
Symmetry | |
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Space Group | P 63 2 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 | PIXEL | DECTRIS PILATUS 6M | 2016-11-12 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) | 0.9763 | PETRA III, EMBL c/o DESY | P13 (MX1) |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym 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 | 3.682 | 97.361 | 93 | 0.111 | 0.111 | 9.8 | 6.3 | 8246 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 3.682 | 4.05 | 59.5 | 1.349 | 1.349 | 1.5 | 7.4 |
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 | 4NFU | 3.682 | 72.94 | 1.35 | 8238 | 800 | 75.5 | 0.246 | 0.242 | 0.287 |
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 | 11.016 |
f_angle_d | 0.608 |
f_chiral_restr | 0.041 |
f_plane_restr | 0.005 |
f_bond_d | 0.002 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 5893 |
Nucleic Acid Atoms | |
Solvent Atoms | |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
XDS | data reduction |
autoPROC | data scaling |
Aimless | data scaling |
PHASER | phasing |
Coot | model building |
autoPROC | data reduction |
Aimless | data scaling |
STARANISO | data scaling |