7S7A
Crystal structure of CDK2 liganded with compound EF3019
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 291 | 4.5mg/mL CDK2 protein crystalized under 25mM Na/K phosphate, 25mM Hepes Na, pH 7.5, 5% v/v PEG3350 was soaked overnight with 5mM EF3109 in 50mM Hepes Na, pH 7.5, 10% v/v PEG3350 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.08 | 40.8 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 53.92 | α = 90 |
b = 72.17 | β = 90 |
c = 72.53 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
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 | 93 | PIXEL | DECTRIS PILATUS 6M | 2020-03-10 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 23-ID-D | 1.0332 | APS | 23-ID-D |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | Rrim I (All) | 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 | 1.7 | 27.77 | 99.69 | 0.045 | 21.14 | 3.3 | 31791 | 28.56 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Rrim I (All) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 1.7 | 1.74 | 0.818 |
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 | THROUGHOUT | 4kd1 | 1.7 | 27.77 | 1.36 | 31722 | 1585 | 99.7 | 0.2075 | 0.2058 | 0.2383 | 36.0614 |
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] | |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2185 |
Nucleic Acid Atoms | |
Solvent Atoms | 115 |
Heterogen Atoms | 37 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
Aimless | data scaling |
PDB_EXTRACT | data extraction |
DIALS | data reduction |
PHENIX | phasing |