8FO6
Nucleotide-free structure of a functional construct of eukaryotic elongation factor 2 kinase.
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 7SHQ | residues 1-80 of chain B were not used |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION | 5.9 | 293 | 100 mM Bis-trispropane, 200 mM NaF, 17.6% PEG-3350 (2protein 1solution) |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.49 | 50.6 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 77.527 | α = 90 |
b = 58.901 | β = 109.67 |
c = 88.394 | 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 EIGER X 16M | Horizontal pre-focus bimorph mirror & KB bimorph mirrors | 2022-05-28 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSLS-II BEAMLINE 17-ID-2 | 0.97934 | NSLS-II | 17-ID-2 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim 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 | |||||
1 | 2.553 | 73.001 | 99.9 | 0.1117 | 0.1227 | 0.05 | 0.996 | 10.33 | 6.09 | 24680 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
2.553 | 2.597 | 100 | 0.7964 | 0.8746 | 0.3566 | 0.838 | 2.31 | 5.87 | 1228 |
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 | 7SHQ | 2.553 | 47.52 | 1.35 | 24650 | 1153 | 99.77 | 0.2176 | 0.2169 | 0.2314 | 60.06 |
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 | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 16.7228 |
f_angle_d | 0.5608 |
f_chiral_restr | 0.0379 |
f_plane_restr | 0.0042 |
f_bond_d | 0.0029 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4739 |
Nucleic Acid Atoms | |
Solvent Atoms | 107 |
Heterogen Atoms | 3 |
Software
Software | |
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Software Name | Purpose |
autoPROC | data processing |
Aimless | data scaling |
TRUNCATE | data processing |
PHENIX | refinement |
XDS | data reduction |
PHASER | phasing |
ISOLDE | refinement |
Coot | model building |