8GM4
Functional construct of the Eukaryotic elongation factor 2 kinase bound to an ATP-competitive inhibitor
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 7SHQ | Only residues 80-148 were used for chain B |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION | 6.2 | 295.15 | Cocktail:16.55% PEG-3350, 200 mM NaF, 100 mM BisTris-Propane Protein sol: 10.3 mg/mL 20 mM Tris pH 7.5, 100 mM NaCl, 3 mM CaCl2, 1mM TCEP, 0.3 mM ADP, 0.3 m Inhibitor , 0.7 % DMSO 2protein/1cocktail (0.2 ul total) |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.64 | 53.11 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 80.544 | α = 90 |
b = 60.684 | β = 111.1 |
c = 88.704 | 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 | 2.009 | 75.133 | 100 | 0.2073 | 0.2274 | 0.0924 | 0.985 | 4.97 | 5.99 | 53518 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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) | ||||||||
2.009 | 2.044 | 100 | 3.6511 | 3.9851 | 1.5825 | 0.311 | 0.68 | 6.13 | 2638 |
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 | 2.12 | 47.73 | 1.34 | 45318 | 2303 | 99.14 | 0.2086 | 0.2071 | 0.2376 | 48.69 |
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 | 5.9337 |
f_angle_d | 0.5148 |
f_chiral_restr | 0.0376 |
f_plane_restr | 0.0034 |
f_bond_d | 0.0027 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4215 |
Nucleic Acid Atoms | |
Solvent Atoms | 362 |
Heterogen Atoms | 51 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
autoPROC | data processing |
Aimless | data scaling |
TRUNCATE | data processing |
XDS | data reduction |
PHASER | phasing |
Coot | model building |