7SHQ
Structure of a functional construct of eukaryotic elongation factor 2 kinase in complex with calmodulin.
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3PDT | 3PDT,3LKM,4KUJ,1IA9,6NX4,4OZS,3RJV |
experimental model | PDB | 3LKM | 3PDT,3LKM,4KUJ,1IA9,6NX4,4OZS,3RJV |
experimental model | PDB | 4KUJ | 3PDT,3LKM,4KUJ,1IA9,6NX4,4OZS,3RJV |
experimental model | PDB | 1IA9 | 3PDT,3LKM,4KUJ,1IA9,6NX4,4OZS,3RJV |
experimental model | PDB | 6NX4 | 3PDT,3LKM,4KUJ,1IA9,6NX4,4OZS,3RJV |
experimental model | PDB | 4OZS | 3PDT,3LKM,4KUJ,1IA9,6NX4,4OZS,3RJV |
experimental model | PDB | 3RJV | 3PDT,3LKM,4KUJ,1IA9,6NX4,4OZS,3RJV |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | MICROBATCH | 6.9 | 298.15 | Cocktail solution: Peg3350: 24% MgCl2: 300 mM BisTris pH 6.9: 100 mM Protein Solution: 11 mg/mL CaM-eEF2Kp1/1 Tris pH 7.5: 20 mM NaCl: 0.1 M CaCl2: 3mM TCEP: 1mM MgCl2: 1.5 mM AMPPNP: 1.0 mM Crystallization conditions: 1/1 Protein/Cocktail under Paraffin Oil in a Greiner 72-Well microbatch plate |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.33 | 47.3 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 58.495 | α = 90 |
b = 58.495 | β = 90 |
c = 365.779 | γ = 120 |
Symmetry | |
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Space Group | P 31 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 PILATUS 6M | 2021-06-18 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSLS-II BEAMLINE 19-ID | 0.97946 | NSLS-II | 19-ID |
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 | 2.34 | 121.9 | 100 | 0.362 | 0.137 | 0.073 | 0.994 | 14.5 | 25.9 | 32010 | 14.98 |
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) | ||||||||
1 | 2.342 | 2.382 | 100 | 1.778 | 1.817 | 0.368 | 0.943 | 2.5 | 24.5 |
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 | 3PDT,3LKM,4KUJ,1IA9,6NX4,4OZS,3RJV | 2.34 | 50.66 | 1.34 | 31982 | 1514 | 99.9 | 0.2304 | 0.2293 | 0.252 | 33.65 |
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 | 6.504 |
f_angle_d | 0.6114 |
f_chiral_restr | 0.0412 |
f_plane_restr | 0.0039 |
f_bond_d | 0.0034 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 5106 |
Nucleic Acid Atoms | |
Solvent Atoms | 143 |
Heterogen Atoms | 8 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
ISOLDE | refinement |
Coot | model building |
MR-Rosetta | phasing |
autoPROC | data scaling |
autoPROC | data reduction |